mtDNA haplogroup X: An ancient link between Europe/Western Asia and North America?

On the basis of comprehensive RFLP analysis, it has been inferred that approximately 97% of Native American mtDNAs belong to one of four major founding mtDNA lineages, designated haplogroups "A"-"D." It has been proposed that a fifth mtDNA haplogroup (haplogroup X) represents a minor founding lineage in Native Americans. Unlike haplogroups A-D, haplogroup X is also found at low frequencies in modern European populations. To investigate the origins, diversity, and continental relationships of this haplogroup, we performed mtDNA high-resolution RFLP and complete control region (CR) sequence analysis on 22 putative Native American haplogroup X and 14 putative European haplogroup X mtDNAs. The results identified a consensus haplogroup X motif that characterizes our European and Native American samples. Among Native Americans, haplogroup X appears to be essentially restricted to northern Amerindian groups, including the Ojibwa, the Nuu-Chah-Nulth, the Sioux, and the Yakima, although we also observed this haplogroup in the Na-Dene-speaking Navajo. Median network analysis indicated that European and Native American haplogroup X mtDNAs, although distinct, nevertheless are distantly related to each other. Time estimates for the arrival of X in North America are 12,000-36,000 years ago, depending on the number of assumed founders, thus supporting the conclusion that the peoples harboring haplogroup X were among the original founders of Native American populations. To date, haplogroup X has not been unambiguously identified in Asia, raising the possibility that some Native American founders were of Caucasian ancestry.     

Genetic differences between Chibcha and Non-Chibcha speaking tribes based on mitochondrial DNA (mtDNA) haplogroups from 21 Amerindian tribes from Colombia

We analyzed the frequency of four mitochondrial DNA haplogroups in 424 individuals from 21 Colombian Amerindian tribes. Our results showed a high degree of mtDNA diversity and genetic heterogeneity. Frequencies of mtDNA haplogroups A and C were high in the majority of populations studied. The distribution of these four mtDNA haplogroups from Amerindian populations was different in the northern region of the country compared to those in the south. Haplogroup A was more frequently found among Amerindian tribes in northern Colombia, while haplogroup D was more frequent among tribes in the south. Haplogroups A, C and D have clinal tendencies in Colombia and South America in general. Populations belonging to the Chibcha linguistic family of Colombia and other countries nearby showed a strong genetic differentiation from the other populations tested, thus corroborating previous findings. Genetically, the Ingano, Paez and Guambiano populations are more closely related to other groups of south eastern Colombia, as also inferred from other genetic markers and from archeological data. Strong evidence for a correspondence between geographical and linguistic classification was found, and this is consistent with evidence that gene flow and the exchange of customs and knowledge and language elements between groups is facilitated by close proximity.     

Possible migration routes into South America deduced from mitochondrial DNA studies in Colombian Amerindian populations

Mitochondrial DNA haplotype studies have been useful in unraveling the origins of Native Americans. Such studies are based on restriction site and intergenic deletion/insertion polymorphisms, which define four main haplotype groups common to Asian and American populations. Several studies have characterized these lineages in North, Central, and South American Amerindian, as well as Na Dene and Aleutian populations. Siberian, Central Asian, and Southeast Asian populations have also been analyzed, in the hope of fully depicting the route(s) of migration between Asia and America. Colombia, a key route of migration between North and South America, has until now not been studied. To resolve the current lack of information about Colombian Amerindian populations, we have investigated the presence of the founder haplogroups in 25 different ethnic groups from all over the country. The present research is part of an interdisciplinary program, Expedición Humana, fostered by the Universidad Javeriana and Dr. J. E. Bernal V. The results show the presence of the four founder A-D Amerindian lineages, with varied distributions in the different populations, as well as the presence of other haplotypes in frequencies ranging from 3% to 26%. These include some unique or private polymorphisms, and also indicate the probable presence of other Asian and a few non-Amerindian lineages. A spatial structure is apparent for haplogroups A and D, and to a lesser extent for haplogroup C. While haplogroup A and D frequencies in Colombian populations from the northwestern side of the Andes resemble those seen in Central American Amerindians more than those seen in South American populations, their frequencies on the southeastern side more closely resemble the bulk of South American frequencies so far reported, raising the question as to whether they reflect more than one migration route into South America. High frequencies of the B lineage are also characteristic of some populations. Our observations may be explained by historical events during the pre-Columbian dispersion of the first settlers and, later, by disruptions caused by the European colonization.     

Unexpected patterns of mitochondrial DNA variation among Native Americans from the southeastern United States

Mitochondrial DNA (mtDNA) haplogroups were determined by restriction fragment length polymorphism-typing for 66 individuals from four southeastern North American populations, and the HVS I portion of the mtDNA control region was sequenced in 48 of these individuals. Although populations from the same geographic region usually exhibit similar haplogroup frequency distributions (Lorenz and Smith [1996] Am. J. Phys. Anthropol. 101:307-323; Malhi et al. [2001] Hum. Biol. 73:17-55), those from the Southeast instead exhibit haplogroup frequency distributions that differ significantly from one another. Such divergent haplogroup frequency distributions are unexpected for the Muskogean-speaking southeastern populations, which share many sociocultural traits, speak closely related languages, and have experienced extensive admixture both with each other and with other eastern North American populations. Independent origins, genetic isolation from other Native American populations due to matrilocality, differential admixture, or a genetic bottleneck could be responsible for this heterogeneous distribution of haplogroup frequencies. Within a given haplogroup, however, the HVS I sequences from the four Muskogean-speaking populations appear relatively similar to one another, providing evidence for close relationships among them and for reduced diversity within haplogroups in the Southeast. Given additional archaeological, linguistic, and ethnographic evidence, these results suggest that a genetic bottleneck associated with the historical population decline is the most plausible explanation for such patterns of mtDNA variation.     

Analysis of admixture and genetic structure of two Native American groups of Southern Argentinean Patagonia

Argentinean Patagonia is inhabited by people that live principally in urban areas and by small isolated groups of individuals that belong to indigenous aboriginal groups; this territory exhibits the lowest population density of the country. Mapuche and Tehuelche (Mapudungun linguistic branch), are the only extant Native American groups that inhabit the Argentinean Patagonian provinces of Río Negro and Chubut. Fifteen autosomal STRs, 17 Y-STRs, mtDNA full length control region sequence and two sets of Y and mtDNA-coding region SNPs were analyzed in a set of 434 unrelated individuals. The sample set included two aboriginal groups, a group of individuals whose family name included Native American linguistic root and urban samples from Chubut, Río Negro and Buenos Aires provinces of Argentina. Specific Y Amerindian haplogroup Q1 was found in 87.5 % in Mapuche and 58.82 % in Tehuelche, while the Amerindian mtDNA haplogroups were present in all the aboriginal sample contributors investigated. Admixture analysis performed by means of autosomal and Y-STRs showed the highest degree of admixture in individuals carrying Mapuche surnames, followed by urban populations, and finally by isolated Native American populations as less degree of admixture. The study provided novel genetic information about the Mapuche and Tehuelche people and allowed us to establish a genetic correlation among individuals with Mapudungun surnames that demonstrates not only a linguistic but also a genetic relationship to the isolated aboriginal communities, representing a suitable proxy indicator for assessing genealogical background.     

Mitochondrial DNA studies show asymmetrical Amerindian admixture in Afro-Colombian and Mestizo populations

The origin of the African populations that arrived on the Colombian coasts at the time of the Spanish conquest and their subsequent settlement throughout the country and interaction with Amerindian and Spanish populations are features that can be analyzed through the study of mitochondrial DNA (mtDNA) markers. For this purpose, the present study investigates the admixture between these populations by analyzing the markers defining the main (A, B, C, D) and minor (X) founder haplogroups in Native Americans, the principal African haplogroup (L), and additional generic markers present in Caucasian (I, J, K, H, T, U, V, W) and minor African lineages (L3). As part of an interdisciplinary research program (the Expedición Humana, furthered by the Universidad Javeriana and directed by J.E. Bernal V.), 159 Afro-Colombians from five populations in which they are the majority and 91 urban Mestizos were studied. No Amerindian haplogroups (A-D, X) were detected in 81% of the Afro-Colombians. In those samples with Amerindian lineages (average 18.8%, with a range from 10% to 43%), haplogroup B predominated. When analyzed for the presence of African haplotypes, Afro-Colombians showed an overall frequency of 35.8% for haplogroup L mtDNAs, although with broad differences between populations. A few Afro-Colombian samples (1.9%) had mutations that have not been described before, and might therefore be considered as previously unsampled African variants or as new mutations arising in the American continent. Conversely, in Mestizos less than 22% of their mtDNAs belonged to non-Amerindian lineages, of which most were likely to be West Eurasian in origin. Haplogroup L mtDNAs were found in only one Mestizo (1.1%), indicating that, if present, admixture with African women would bring in other, rarer African lineages. On the other hand, in an accompanying paper (Keyeux et al. 2002) we have shown that Amerindians from Colombia have experienced little or no matrilineal admixture with Caucasians or Africans. Taken together, these results are evidence of different patterns of past ethnic admixture among Africans, Amerindians, and Spaniards in the geographic region now encompassing Colombia, which is also reflected in much of the region's cultural diversity.     

Major mitochondrial DNA haplotype heterogeneity in highland and lowland Amerindian populations from Bolivia

This study provides the frequencies of four mitochondrial DNA (mtDNA) haplogroups of 233 native South Amerindians in eight populations living in the Beni Department of Bolivia, including six populations not previously studied. Linguistically, these populations belong to the three principal South Amerindian language stocks, Andean, Equatorial-Tucanoan, and Ge-Pano-Carib. Frequency analyses under geographic, historic, linguistic, and genetic configurations using the theta statistic of Weir (Weir 1990) and analysis of molecular variance (AMOVA) show similar results. Results are also similar when phenetic cluster is used. Aymara belongs almost exclusively to haplogroup B, Quechua- and Moseten-speaking tribes belong to haplogroups A and B, but the first tribe presents high frequencies of haplogroup B. Yuracare, Trinitario, and Ignaciano exhibit high frequencies of A, B, and C haplogroups, and the Movima present a large proportion of haplogroup C. There is some correspondence between mtDNA haplogroup frequencies and language affiliation and historical connections, but less so with geographic aspects. The present study provides a context for understanding the relationship between different Amerindian populations living in a multiethnic area of Bolivia.     

Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA

We examined mitochondrial DNA (mtDNA) haplogroup and haplotype diversity in 188 individuals from three Chibchan (Kogi, Arsario, and Ijka) populations and one Arawak (Wayuú) group from northeast Colombia to determine the biological relationship between lower Central American and northern South American Chibchan speakers. mtDNA haplogroups were obtained for all individuals and mtDNA HVS-I sequence data were obtained for 110 samples. Resulting sequence data were compared to 16 other Caribbean, South, and Central American populations using diversity measures, neutrality test statistics, sudden and spatial mismatch models, intermatch distributions, phylogenetic networks, and a multidimensional scaling plot. Our results demonstrate the existence of a shared maternal genetic structure between Central American Chibchan, Mayan populations and northern South American Chibchan-speakers. Additionally, these results suggest an expansion of Chibchan-speakers into South America associated with a shift in subsistence strategies because of changing ecological conditions that occurred in the region between 10,000-14,000 years before present.     

Distribution of four founding mtDNA haplogroups among Native North Americans

The mtDNA of most Native Americans has been shown to cluster into four lineages, or haplogroups. This study provides data on the haplogroup affiliation of nearly 500 Native North Americans including members of many tribal groups not previously studied. Phenetic cluster analysis shows a fundamental difference among 1) Eskimos and northern Na-Dene groups, which are almost exclusively mtDNA haplogroup A, 2) tribes of the Southwest and adjacent regions, predominantly Hokan and Uto-Aztecan speakers, which lack haplogroup A but exhibit high frequencies of haplogroup B, 3) tribes of the Southwest and Mexico lacking only haplogroup D, and 4) a geographically heterogeneous group of tribes which exhibit varying frequencies of all four haplogroups. There is some correspondence between language group affiliations and the frequencies of the mtDNA haplogroups in certain tribes, while geographic proximity appears responsible for the genetic similarity among other tribes. Other instances of similarity among tribes suggest hypotheses for testing with more detailed studies. This study also provides a context for understanding the relationships between ancient and modern populations of Native Americans. © 1996 Wiley-Liss, Inc.     

Distribution of mtDNA haplogroup X among Native North Americans.

Mitochondrial DNA (mtDNA) samples of 70 Native Americans, most of whom had been found not to belong to any of the four common Native American haplogroups (A, B, C, and D), were analyzed for the presence of Dde I site losses at np 1715 and np 10394. These two mutations are characteristic of haplogroup X which might be of European origin. The first hypervariable segment (HVSI) of the non-coding control region (CR) of mtDNA of a representative selection of samples exhibiting these mutations was sequenced to confirm their assignment to haplogroup X. Thirty-two of the samples exhibited the restriction site losses characteristic of haplogroup X and, when sequenced, a representative selection (n = 11) of these exhibited the CR mutations commonly associated with haplogroup X, C --> T transitions at np 16278 and 16223, in addition to as many as three other HVSI mutations. The wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestor/descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups.     

Is haplogroup X present in extant South American Indians?

A total of 1,159 mitochondrial DNA samples from two Mongolian, two Siberian, and 25 South Native American populations was surveyed for the presence of the C16278T mutation, frequently found in haplogroup X. Material from 25 carriers of that mutation was then sequenced for the hypervariable segment I (HVS-I) control region, and those that still were not classifiable in classical Amerindian haplogroups were further studied. The tests involved all the control region, as well as the presence of characteristic mutations in seven coding fragments, totalling 5,760 base pairs. The results indicate that haplogroup X is not present in these samples.     

Genetic diversity in an Andean population from Peru and regional migration patterns of Amerindians in South America: data from Y chromosome and mitochondrial DNA

The genetic variability of a Quechua-speaking Andean population from Peru was examined on the basis of four Y chromosome markers and restriction sites that define the Amerindian mitochondrial DNA (mtDNA) haplogroups. Forty-nine out of 52 (90.4%) individuals had mtDNA which belonged to one of the four common Amerindian haplogroups, with 54% of the samples belonging to haplogroup B. Among 25 males, 12 had an Amerindian Y chromosome, which exists as four haplotypes defined on the basis of the DYS287, DYS199, DYS392 and DYS19 markers, three of which are shared by Amazonian Amerindians. Thus, there is a clear directionality of marriages, with an estimated genetic admixture with non-Amerindians that is 9 times lower for mtDNA than for Y chromosome DNA. The comparison of mtDNA of Andean Amerindians with that of people from other regions of South America in a total of 1,086 individuals demonstrates a geographical pattern, with a decreasing frequency of A and C haplotypes and increasing frequency of the D haplotype from the north of the Amazon River to the south of the Amazon River, reaching the lowest and the highest frequencies, respectively, in the more southern populations of Chile and Argentina. Conversely, the highest and lowest frequencies of the haplogroup B are found, respectively, in the Andean and the North Amazon regions, and it is absent from some southern populations, suggesting that haplotypes A, C and D, and haplotype B may have been dispersed by two different migratory routes within the continent.     

Brief communication: molecular analysis of the Kwäday Dän Ts'finchi ancient remains found in a glacier in Canada

DNA was extracted from the frozen remains of a man found in the northwest corner of British Columbia, Canada, in 1999. His clothing was radiocarbon-dated at ca. 550 years old. Nitrogen and carbon content in whole bone and collagen-type residue extracted from both bone and muscle indicated good preservation of proteinaceous macromolecules. Restriction enzyme analysis of mitochondrial DNA (mtDNA) determined that the remains belong to haplogroup A, one of the four major Native American mtDNA haplogroups. Data obtained by PCR direct sequencing of the mtDNA control region, and by sequencing the clones from overlapping PCR products, were duplicated by an independent laboratory. Comparison of these mtDNA sequences with those of North American, Central American, South American, East Siberian, Greenlandic, and Northeast Asian populations indicates that the remains share an mtDNA type with North American, Central American, and South American populations.     

mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans.

The mtDNA variation of 411 individuals from 10 aboriginal Siberian populations was analyzed in an effort to delineate the relationships between Siberian and Native American populations. All mtDNAs were characterized by PCR amplification and restriction analysis, and a subset of them was characterized by control region sequencing. The resulting data were then compiled with previous mtDNA data from Native Americans and Asians and were used for phylogenetic analyses and sequence divergence estimations. Aboriginal Siberian populations exhibited mtDNAs from three (A, C, and D) of the four haplogroups observed in Native Americans. However, none of the Siberian populations showed mtDNAs from the fourth haplogroup, group B. The presence of group B deletion haplotypes in East Asian and Native American populations but their absence in Siberians raises the possibility that haplogroup B could represent a migratory event distinct from the one(s) which brought group A, C, and D mtDNAs to the Americas. Our findings support the hypothesis that the first humans to move from Siberia to the Americas carried with them a limited number of founding mtDNAs and that the initial migration occurred between 17,000-34,000 years before present.     

mtDNA microevolution in Southern Chile's archipelagos

The genetic variability of four predominantly Indian populations of southern Chile's archipelagos was examined by determining the frequencies of four mitochondrial DNA haplogroups that characterize the American Indian populations. Over 90% of the individuals analyzed presented Native American mtDNA haplogroups. By means of an unweighted group pair method with arithmetic mean (UPGMA) dendrogram, a principal component analysis (PCA) derived from a distance matrix of mtDNA, and the exact test of population differentiation, we are able to prove the existence of a North‐South cline. The populations in the northern part of the archipelagos are genetically similar to the Huilliche tribe, while the groups from the South are most closely related to the Fueguino tribe from the extreme South of Chile, and secondarily to the Pehuenche and Mapuche, who are found to the North and East of Chiloé archipelago. These results are consistent with a colonization of the southern archipelagos from Tierra del Fuego. We evaluate the evolutionary relationships of the population of the Chiloé area to groups from other geographic areas of Chile, using analysis of molecular variance (AMOVA). Three Amerindian clusters are identified: one formed by the Aymará and Atacameño, a second by the Huilliche, and a third including the Mapuche, Pehuenche, and Fueguino tribes, and the population inhabiting the South of the Chiloé arcipelago. These groups exhibit a North‐South gradient in the frequency of haplogroup B, confirmed by F_ST tests. Am J Phys Anthropol, 2006 © 2005 Wiley‐Liss, Inc.     

Linguistic and maternal genetic diversity are not correlated in Native Mexicans

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.     

Microevolution in prehistoric Andean populations: chronologic mtDNA variation in the desert valleys of northern Chile

Archeological evidence suggests that the iconographic and technological developments that took place in the highlands around Lake Titicaca in the Central Andean region had an influence on the cultural elaborations of the human groups in the valleys and the Pacific coast of northern Chile. In a previous communication, we were able to show, by means of a distance analysis, that a craniofacial differentiation accompanied the process of cultural evolution in the valleys (Rothhammer and Santoro [2001] Lat. Am. Antiq. 12:59-66). Recently, numerous South Amerindian mtDNA studies were published, and more accurate molecular techniques to study ancient mtDNA are available. In view of these recent developments, we decided 1) to study chronological changes of ancient mtDNA haplogroup frequencies in the nearby Lluta, Azapa, and Camarones Valleys, 2) to identify microevolutionary forces responsible for such changes, and 3) to compare ancient mtDNA haplogroup frequencies with previous data in order to validate craniometrical results and to reconstruct the biological history of the prehistoric valley groups in the context of their interaction with culturally more developed highland populations. From a total of 97 samples from 83 individuals, 68 samples (61 individuals) yielded amplifications for the fragments that harbor classical mtDNA markers. The haplogroup distribution among the total sample was as follows: 26.2%, haplogroup A; 34.4%, haplogroup B; 14.8%, haplogroup C; 3.3%, haplogroup D; and 21.3%, other haplogroups. Haplogroup B tended to increase, and haplogroup A to decrease during a 3,900-year time interval. The sequence data are congruent with the haplogroup analysis. In fact, the sequencing of hypervariable region I of 30 prehistoric individuals revealed 43 polymorphic sites. Sequence alignment and subsequent phylogenetic tree construction showed two major clusters associated with the most common restriction haplogroups. Individuals belonging to haplogroups C and D tended to cluster together with nonclassical lineages.     

Uniparental genetic markers in South Amerindians

A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.     

Diversity and Age of the Four Major mtDNA Haplogroups, and Their Implications for the Peopling of the New World

Despite considerable investigation, two main questions on the origin of Native Americans remain the topic of intense debate-namely, the number and time of the migration(s) into the Americas. Using the 720 available Amerindian mtDNA control-region sequences, we reanalyzed the nucleotide diversity found within each of the four major mtDNA haplogroups (A-D) thought to have been present in the colonization of the New World. We first verified whether the within-haplogroup sequence diversity could be used as a measure of the haplogroup's age. The pattern of shared polymorphism, the mismatch distribution, the phylogenetic trees, the value of Tajima's D, and the computer simulations all suggested that the four haplogroups underwent a bottleneck followed by a large population expansion. The four haplogroup diversities were very similar to each other, offering a strong support for their single origin. They suggested that the beginning of the Native Americans' ancestral-population differentiation occurred approximately 30,000-40,000 years before the present (ybp), with a 95%-confidence-interval lower bound of approximately 25,000 ybp. These values are in good agreement with the New World-settlement model that we have presented elsewhere, extending the results initially found for haplogroup A to the three other major groups of mtDNA sequences found in the Americas. These results put the peopling of the Americas clearly in an early, pre-Clovis time frame.     

Asian affinities and continental radiation of the four founding Native American mtDNAs.

The mtDNA variation of 321 individuals from 17 Native American populations was examined by high-resolution restriction endonuclease analysis. All mtDNAs were amplified from a variety of sources by using PCR. The mtDNA of a subset of 38 of these individuals was also analyzed by D-loop sequencing. The resulting data were combined with previous mtDNA data from five other Native American tribes, as well as with data from a variety of Asian populations, and were used to deduce the phylogenetic relationships between mtDNAs and to estimate sequence divergences. This analysis revealed the presence of four haplotype groups (haplogroups A, B, C, and D) in the Amerind, but only one haplogroup (A) in the Na-Dene, and confirmed the independent origins of the Amerinds and the Na-Dene. Further, each haplogroup appeared to have been founded by a single mtDNA haplotype, a result which is consistent with a hypothesized founder effect. Most of the variation within haplogroups was tribal specific, that is, it occurred as tribal private polymorphisms. These observations suggest that the process of tribalization began early in the history of the Amerinds, with relatively little intertribal genetic exchange occurring subsequently. The sequencing of 341 nucleotides in the mtDNA D-loop revealed that the D-loop sequence variation correlated strongly with the four haplogroups defined by restriction analysis, and it indicated that the D-loop variation, like the haplotype variation, arose predominantly after the migration of the ancestral Amerinds across the Bering land bridge.