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Am J Hum Genet. Nov 2000; 67(5): 1277–1286.
Published online Oct 13, 2000. doi:  10.1016/S0002-9297(07)62955-3
PMCID: PMC1288567

Autosomal, mtDNA, and Y-Chromosome Diversity in Amerinds: Pre- and Post-Columbian Patterns of Gene Flow in South America


To evaluate sex-specific differences in gene flow between Native American populations from South America and between those populations and recent immigrants to the New World, we examined the genetic diversity at uni- and biparental genetic markers of five Native American populations from Colombia and in published surveys from native South Americans. The Colombian populations were typed for five polymorphisms in mtDNA, five restriction sites in the β-globin gene cluster, the DQA1 gene, and nine autosomal microsatellites. Elsewhere, we published results for seven Y-chromosome microsatellites in the same populations. Autosomal polymorphisms showed a mean GST of 6.8%, in agreement with extensive classical marker studies of South American populations. MtDNA and Y-chromosome markers resulted in GST values of 0.18 and 0.165, respectively. When only Y chromosomes of confirmed Amerind origin were used in the calculations (as defined by the presence of allele T at locus DYS199), GST increased to 0.22. GST values calculated from published data for other South American natives were 0.3 and 0.29 for mtDNA and Amerind Y chromosomes, respectively. The concordance of these estimates does not support an important difference in migration rates between the sexes throughout the history of South Amerinds. Admixture analysis of the Colombian populations suggests an asymmetric pattern of mating involving mostly immigrant men and native women.


Genetic data have been used for several decades in the study of human evolutionary history (Cavalli-Sforza 1998; Jorde et al. 1998; Ruiz-Linares 1999). Most often, population analyses have examined allele frequencies at autosomal (biparental) genetic markers (Cavalli-Sforza et al. 1994). The incorporation of mtDNA during the 1980s added a powerful tool to the geneticist's tool kit, since mtDNA does not recombine and is transmitted only by women (Stoneking and Soodyall 1996). More recently, the increasing number of polymorphic markers identified on the nonrecombining region of the Y chromosome is allowing analyses of male lineages along the lines of those performed using mtDNA (Hammer and Zegura 1997). Furthermore, the comparative analysis of markers on autosomes, mtDNA, and the Y chromosome now enables the scrutiny of male and female demographic patterns.

Using this approach, Seielstad et al. (1998) proposed that women had a higher migration rate than men throughout human evolution. Those authors observed that the differentiation of allele frequencies between populations is often much greater for Y-chromosome than for mtDNA polymorphisms. On a worldwide scale, single nucleotide polymorphisms showed a level of population structure that was 3.5 times higher for Y-linked than for mtDNA markers. A greater differentiation of allele frequencies at Y-linked microsatellites (STRs) than at autosomal STRs was also reported for a set of African populations. Finally, it was observed that, in Europe, the greater genetic differentiation of populations at increasing geographic distance was more pronounced for Y chromosome than for nuclear or mitochondrial markers. Although a smaller effective population size for men than for women, due to polygyny, could be involved in producing these patterns of population structure, the magnitude of the difference across markers was deemed to be incompatible with polygyny being solely responsible. A preferred explanation is that these differences are due mostly to a lower migration rate of men. This observation might relate to the well-known phenomenon of patrilocality (the tendency for women to move into the locality inhabited by their male partners), which has been documented in about two-thirds of human populations (Murdock 1981).

Comparison of uni- and biparental genetic markers has also allowed the study of differences in male/female gene flow during more recent times. For example, analyses of mtDNA and autosomal markers in Mexican and Mexican American populations has revealed a frequency of Amerind mtDNA lineages in them of ~90% (Merriwether et al. 1997; Green et al. 2000). This is considerably higher than was expected on the basis of autosomal estimates of Amerind admixture for these populations of ~30%. The difference is indicative of directional mating involving preferentially immigrant men and Amerind women. Similarly, the analysis of sex-specific and autosomal markers in Brazilian individuals of African ancestry evidenced a substantial European admixture that was mediated mostly through men (Bortolini et al. 1999).

Thus far, no comparison of uni- and biparental genetic diversity has been made in the same Native American populations. Here we examine five Colombian native populations using mtDNA, autosomal, and Y-chromosome markers. We use these and published data to compare male and female migration rates during the evolution of native South American populations. Most of the Colombian Amerind populations examined show some degree of admixture, and these data are also informative in relation to the pattern of gene flow between natives and nonnative immigrants having occurred during the past few centuries.

Subjects and Methods

Populations Studied

Five Native American populations living in “Resguardos” (native territories) from Colombia were examined in this study. These populations were selected on the basis of their geographic dispersion within Colombia, their linguistic diversity, and their relatively large population size (table 1 and fig. 1). They include representatives of three of the four major linguistic subfamilies present in South America except Ge-Pano-Carib (Ruhlen 1991). The Zenu (also Senu or Sinu) currently speak only Spanish, and it is unclear what would be the linguistic affiliation of the language once spoken by them. According to Loukotka and Wilbert (1968), no record exists of the Zenu language. Nevertheless, Voegelin and Voegelin (1977) classify Zenu as a Carib language and indicate that Nutabe is a dialect of Zenu. However, this is in disagreement with Greenberg’s classification, which includes Nutabe as a Chibchan language (Ruhlen 1991).

Figure  1
Map of Colombia showing the approximate geographic location of the five Amerind populations examined. The number of samples initially available for study is indicated in parentheses.
Table 1
Census Size and Linguistic Affiliation of the Colombian Amerind Populations Examined

In every case, blood samples were collected from unrelated individuals. Each individual provided informed consent (this research received ethical approval of the Bioethics committee of the Universidad de Antioquia). Ticuna (also Tikuna, Tukuna, or Tucuna) samples were collected from the settlements of Arara (n=50) and Cotuhé (n=50), Departmento del Amazonas. Wayuu (also Guajiro, Goajiro, or Guajira) samples were collected in three localities: Guareripa (n=18), La Loma (n=20), and Ankalabary (n=8), in the Departamento de la Guajira. Ingano (also Inga) samples were collected in San Miguel (n=10) and Sibundoy (n=23), Departamento del Putumayo. Zenu samples (n=150) were collected in San Andrés de Sotavento, Departamento de Córdoba. Embera (also Catíos, Katío, Chamí, or Chocó) samples (n=34) were collected in Dabeiba, Departamento de Antioquia. DNA was extracted using standard protocols. Because of limited DNA availability, not all samples could be tested for every marker.

Autosomal Microsatellite Markers

The loci examined were LIPC, D15S100, D15S148, D15S102, D15S117, D15S125, D13S270, D13S126, and GABR3. These nine loci were included in the population survey of Bowcock et al. (1994), which included samples from Africa (Lisongo, Biaka, and Mbuti pygmies), America (Maya, Karitiana, and Surui), Asia (Cambodian, Chinese, and Japanese), Europe (Italian and northern European), and Oceania (Australian, Melanesian, and New Guinean). Microsatellites were typed radioactively or by fluorescent methods, using the primers and PCR conditions described in the Genome Database.

β-globin RFLPs

Five restriction-site polymorphisms were typed in the β-globin gene cluster by enzyme digestion of PCR products. The sites examined were HincII (5′ of ε), XmnI (5′ of Gγ), HindIII (in IVS-II of the Aγ and Gγ genes), and HincII (3′ of ψβ). These polymorphic sites enable the identification of most of the 16 β-globin cluster haplotypes described in surveys of world populations (Flint et al. 1993). PCR primers, amplification conditions, and expected band sizes were as reported by Sutton et al. (1989). After amplification, PCR products were digested with the appropriate enzyme, run on agarose gels, and visualized by ethidium bromide UV fluorescence. Haplotype frequencies were calculated using the approach of Clark (1990). In ~20% of chromosomes, a restriction pattern was consistent with several haplotypes. In those cases, haplotype designations gave preference to those previously identified in Native Americans.


Allelic variants at the DQA1 locus were typed by dot-blot oligonucleotide hybridization, using the PCR primers, probes, and hybridization conditions recommended by the 12th International Histocompatibility Workshop.

mtDNA Polymorphisms

Four restriction sites and the 9-bp COII/tRNALys intergenic deletion variant were typed by PCR and agarose electrophoresis. The enzymes used and the location of the restriction sites examined (following Anderson’s coordinates) were HaeIII (663 bp), HincII (3,259 bp), AluI (5,176 bp), and HaeIII (6,517 bp). Experimental conditions were as described by Bailliet et al. (1994).

Data Analysis

Genetic diversity was estimated as n/(n-1)(1-Σp2i), where n is the sample size and pi is the estimated allele frequency of allele i. In all cases (including linked markers), diversity was calculated for each individual polymorphism. Population structure was estimated by GST, defined as (HT-HS)/HT, where HT and HS represent the expected heterozygosity under Hardy-Weinberg equilibrium for the total sample and the mean expected heterozygosity across populations, respectively (Nei 1987). Effective number of migrants (Nm) was calculated on the basis of Wright’s island-migration model (Nei 1987). Ignoring mutation, at migration-drift equilibrium, the expectation is that GST=1/(4Nm+1) for autosomal markers and GST=1/(Nm+1) for uniparental markers. Confidence intervals around estimates of population structure were obtained by bootstrapping across loci. Differences between estimates were not considered significant if 95% confidence intervals overlapped (Weir 1996). For autosomal and Y-chromosome data, admixture estimation was performed by a least-squares approximation (Long 1991), using allele frequencies at each marker (i.e., haplotypic information was not used). For admixture calculations, classical marker data for 11 systems (ABO, Fy, Di, Tf, Rh, Hb, P, Gc, Kidd, Kell, and MN) were obtained by standard immunological and electrophoretic methods for the three populations sampled by N.R.M. and A.R.-L. (Embera, Inga, and Ticuna). Calculations were made using programs in the software packages ARLEQUIN (Schneider et al. 2000), GDA (Lewis and Zaykin 2000), GENETIX (Laboratoire Génome et Populations 2000), DISPAN (Ota 1993), RST CALC (Goodman 1997), and ADMIX (Long 1991).


Autosomal Microsatellites

Figure 2 depicts the genetic relatedness of the 5 Colombian populations examined and of the 14 populations examined by Bowcock et al. (1994), on the basis of allele frequencies at nine STRs. This tree is consistent with that obtained by Bowcock et al. (1994), in that all populations cluster according to their continent of origin, and African populations, as a whole, appear to be more distantly related to the other populations. The separation of non-African continental populations is mostly undefined. Of interest, South American populations appear in a discrete cluster separate from the Mayan population from Central America. As expected, the bootstrap support for this tree is generally lower than that obtained by Bowcock et al. (1994), using 30 STRs.

Figure  2
Neighbor-joining tree, based on nine autosomal microsatellites, relating 19 native populations from around the world. The tree was constructed from a pair-wise distance matrix, calculated using the DA genetic distance (Nei 1987). Numbers indicate percent ...

β-Globin RFLPs

Table 2 compares haplotype frequencies at the β-globin gene cluster in the five Colombian populations with those reported for other Amerinds and for representative European and African populations. The haplotype frequencies observed in the Colombian populations agree with those seen in other Amerinds in showing a predominance of haplotypes 2 and 6. However, apart from the Ticuna, the populations we typed show less-extreme frequencies of these two haplotypes, together with the presence of additional haplotypes. Some degree of admixture is suggested by the presence in the Colombian populations (except in the Ticuna) of haplotypes 3 or 5, which are generally rare in Amerinds but have relatively high frequencies in African or European populations.

Table 2
Percentage Frequency of β-Globin Gene Cluster Haplotypes in Native Populations from South America, Europe, and Africa[Note]

mtDNA Haplogroups

Table 3 shows the frequency in the Amerinds tested of the four major founder mtDNA lineages that have been identified in Native Americans (Torroni et al. 1993; Merriwether and Ferrell 1996). All the Ticuna individuals examined carry haplotypes belonging to these haplogroups. In the other populations, [less-than-or-eq, slant]5% of individuals carry haplotypes lacking mutations diagnostic of founder lineages. These could represent novel founder haplogroups, back mutations at one of the diagnostic sites, or non-Amerind admixture. Preliminary mtDNA D-loop sequence analysis in 17 Colombian Amerind populations, including those examined here, suggests that haplotypes lacking characteristic RFLP changes mostly represent back mutations of C lineages (A.R.-L., unpublished data).

Table 3
Percentage Frequency of mtDNA RFLP Haplogroups

Intrapopulation Diversity

Table 4 compares the genetic diversity of the Colombian populations for the different sets of markers examined, including values calculated from Y-chromosome STR (Y-STR) data reported elsewhere (Ruiz-Linares et al. 1999). The Embera show some reduction of diversity for all systems examined, except for the β-globin gene cluster RFLPs, thus suggesting that this settlement is likely to have undergone a recent bottleneck. At these same markers, the Ticuna show a marked reduction in diversity. Only one Ticuna settlement was typed for the β-globin gene cluster RFLPs, and this settlement also shows some reduction in Y-STR diversity (data not shown), suggesting another instance of a recent population constriction.

Table 4
Genetic Diversity, Estimated with Uniparental and Biparental Genetic Markers

The mean diversity values obtained for South America with the Y-chromosome and autosomal STR loci were 0.542 and 0.697, respectively. These values are similar to those reported for the same markers in other continents except for Africa, which shows a higher level of diversity (Bowcock et al. 1994; Jorde et al. 2000).

Interpopulation Diversity

Table 5 shows the level of genetic structure detected with the different sets of markers typed in the Colombian populations. The mean GST value observed for Y STRs is very similar to that obtained with mtDNA (0.165 vs. 0.18, respectively). These values are considerably higher than the mean value obtained from nuclear markers in the same populations (0.068). The increased variability of allele frequencies at uniparental markers is expected, given their smaller effective population size relative to autosomes. Noticeably, the estimated number of migrants obtained with the different genetic systems is very similar (Nm≈4). A bootstrap analysis indicates that the difference between estimates of population structure based on mtDNA and Y markers are not statistically significant.

Table 5
GST and Effective Nm Estimated with Uni- and Biparental Genetic Markers for Native Populations from Colombia And South America

Table 5 also shows GST values estimated from data of previous surveys in other native South American populations for mtDNA, Y-chromosome STRs, and two of the three autosomal systems examined in the Colombian populations. The level of genetic structure observed in South America is generally somewhat higher than that for the Colombian populations, possibly because of the larger number of populations included and their wider geographic distribution. However, the estimated effective number of migrants is again similar for the different genetic systems (Nm≈1–3). Specifically, for mtDNA and Y STRs, the value of Nm is very close (2.5 and 2.3, respectively).

Admixture Analyses

Bi- and uniparental markers were also used to estimate levels of admixture, and results are shown in table 6. In the case of the mtDNA polymorphisms, the Amerind contribution was simply taken as the aggregate frequency of the major founding lineages, with allowance for the possibility that the other lineages observed could have an Amerind, African, or European origin. Although the admixture estimates carry large error margins, they broadly indicate that all populations, except the Ticuna, have considerable non-Amerind admixture (~20%–30%, on the basis of the autosomal results). This is in agreement with the greater geographical isolation of the Ticuna, who live in a remote Amazonian location (fig. 1). In the admixed populations, the Amerind component detected with nuclear markers is always smaller than that observed with mtDNA. This suggests that the non-Amerind component of the Native American gene pool was probably introduced through men. This is in agreement with the Y-STR–based estimates of admixture which, apart from the Ingano, show the smallest Amerind component of the three sets of markers. Estimates for the Ingano have the poorest fit to the admixture model used, as indicated by their relatively high mean square error (table 6). Taken together, these results are consistent with an asymmetric pattern of gene flow involving mainly immigrant men and Native American women.

Table 6
Admixture Estimates Based on Bi- and Uniparental Genetic Markers


The comparison of genetic structure parameters based on uni- and biparental genetic markers, such as that made by Seielstad et al. (1998), has been criticized on the grounds that they did not include uniform sets of markers and populations (Stoneking 1998). In this article, we examined population structure for native South Americans on the basis of published data, as well as by typing a uniform set of markers in the same five Amerind populations. The level of genetic structure detected with autosomal markers in Colombian Amerinds is highly consistent with the one estimated for South America based on a large number of classical markers and populations (~6%) (Cavalli-Sforza et al. 1994). This figure is about twice the value observed in other continents, confirming that native populations from South America show the greatest differentiation in allele frequencies of any continent. This important variation in allele frequencies most likely reflects strong drift, probably because of the small effective size of tribal groups and the common occurrence of founder effects throughout much of the evolutionary history of Amerind populations.

Estimates of population structure based on mtDNA and Y markers were found to be similar to each other (GST of 0.18 vs. 0.165, respectively), the difference not being statistically significant. This observation does not support an important difference in the long-term migration rate of men and women between the populations examined. However, the analysis of table 6 indicates that admixture could particularly affect estimates of population subdivision based on Y chromosome markers. We thus repeated the population-structure estimation, using only Y chromosomes of definite Amerind ancestry—those carrying allele T at locus DYS199 (Ruiz-Linares et al. 1999). This reduced the Y-chromosome data set by ~50%, and we also excluded the Ingano from the analysis, because, in that population, only one chromosome with the DYS199T allele was detected. In this restricted data set, GST increases slightly relative to that obtained when all the data are used (0.226 vs. 0.165, respectively), but the level of population structure is, again, not significantly different from that detected with mtDNA. As shown in table 5, using data from a survey of DYS199T chromosomes in 12 native South American populations, we obtained a GST of 0.30, which is almost identical to the value obtained from extensive surveys of mtDNA variation in South American natives (~ 0.29). Because the Ticuna show no evidence of admixture, we also examined levels of population structure between the two settlements sampled for this population. We obtained a GST for autosomal microsatellites of 0.017. This value is consistent with a GST of 0.02 that we calculated, using data for 15 classical markers reported in six Ticuna settlements from Brazil (Neel et al. 1980). GST estimates based on mtDNA and Y-chromosome markers in the Colombian Ticuna were, respectively, 0.238 and 0.205, again indicating no significant difference in population-structure estimates across markers.

It has been suggested that biallelic markers on the Y chromosome show, on a worldwide scale, a higher level of population structure than Y STRs (Jorde et al. 2000). This difference might relate to the specific mutational properties of the markers, particularly the high mutation rate at STR loci and their propensity to recurrent mutation. To assess the effect of mutation on our estimates, we evaluated population structure on the basis of the Colombian Y-STR data, using the RST statistic of Slatkin (1995), which incorporates stepwise mutations. We obtained RST values of 0.2 and 0.23, using, respectively, all Y chromosomes or only those carrying the DYS199 T allele. The increase seen for the full data set relative to a GST estimate of 0.165 is probably due to the inclusion of some highly divergent haplotypes resulting from admixture. The almost identical GST and RST values obtained with the restricted data set (0.226 vs. 0.23, respectively) suggests that mutation has had little effect on the level of population structure detected. Furthermore, there is no significant correlation between estimates of population structure and locus variability (data not shown)—thus, there seems to be no evidence that our findings are strongly influenced by the mutational characteristics of the Y-STR loci examined.

In conclusion, our results suggest that there has been no important difference in the migration rate of males and females throughout the history of native South American populations. This could be indicating that neither matrilocality nor patrilocality has predominated. In fact, of the 34 South Amerind populations examined in the ethnographic study of Burton et al. (1996), half were considered predominantly patrilocal and half predominantly matrilocal. There would thus seem to be a concordance between the type of social organization and the level of genetic structure detected with different types of genetic markers, as reported by Seielstad et al. (1998). However, ethnographic studies mostly document interactions occurring between groups within populations, and it is not clear what type of interaction predominates between populations, which is the level we have examined, or the effect that local interactions could have on a wider geographic scale (Stoneking 1998).

Admixture analysis suggests a pattern of directional mating that preferentially involved immigrant men and native women. Although it would be desirable to expand sample sizes, in order to have more accurate estimates of admixture, the same pattern has been detected in non-Amerind populations from Mexico (Merriwether et al. 1997; Green et al. 2000) and Colombia (Carvajal-Carmona et al. 2000). This observation agrees with historical records showing that during the colonial period (late 15th to early 19th centuries), most of the immigrants to Spanish America were male (Sanchez-Albornoz 1977). This trend is also likely to have been reinforced by the preferential incorporation of immigrant women and their descendants into criollo society rather than into native American populations. The analysis of uniparental genetic markers in a non-Amerind population from Colombia has shown that Amerind male lineages have almost entirely disappeared from that population but that, at the mtDNA level, Amerind lineages are by far predominant (Carvajal-Carmona et al. 2000). This suggests a marked pattern of directional mating in which native women and immigrant men established neo-American populations. Concomitant with the demographic collapse of Amerinds during the first century of contact, this process seems to have led to the virtual “absorption” (through women) of native populations into the criollo population. Perhaps not surprisingly, the results presented here suggest that South Amerinds who still maintain their identity have frequently been exposed to similar demographic pressures.


We would especially like to thank the populations that participated in this study and all those involved in fieldwork. Francisco M. Salzano improved an earlier version of the manuscript. We thank Merritt Ruhlen for information on the possible linguistic affiliation of the Zenu and Julia Bodmer for HLA workshop information for typing locus DQA1. Primers for the typing of autosomal microsatellites were provided by the International Center for Genetic Engineering and Biotechnology, Trieste, Italy. This work was funded by Colciencias (grant 1115-05-132-94) and Universidad de Antioquia (CODI grants CPT 9811, 9812, and 9914). M.-C.B. is supported by a Wellcome Trust Travelling Research Fellowship (grant 011589) and Conselho Nacional de Desenvolvimiento Científico e Tecnológico.

Electronic-Database Information

The URL for data in this article is as follows:

The Genome Database, http://www.gdb.org/


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