Introduction
============

Native Americans have been the subject of a large number of population genetic studies because of particular characteristics: (a) there are groups among them that until recently had a hunter-gatherer way of living with only incipient agriculture, typical of our ancestors, (b) they show considerable interpopulation but low intrapopulation variability, and (c) since until recently they could not write there is no written record of their history, except for those of non-Amerindian colonizers. Biological studies can therefore be used to investigate their past.

The first genetic studies examined the variability in blood groups and proteins and have been summarized in [@b78-gmb-35-2-365] and [@b22-gmb-35-2-365]. The advent of modern molecular biology, which allows direct, detailed DNA analysis, has opened new possibilities for investigating these populations.

DNA studies can basically be divided into two groups: those involving autosomal markers and those involving uniparental (Y-chromosome, mitochondrial DNA) markers. The latter are important because they can provide a clear-cut pattern of historical events that is not clouded by recombination factors. For Amerindians, the number of reviews that have dealt with these markers is not large or comprehensive. For the Y-chromosome, [@b16-gmb-35-2-365] considered 438 individuals from 23 Southern and one Northern Amerindian populations who were screened for eight single nucleotide polymorphisms (SNPs) and six short tandem repeat/microsatellite (STR) loci, and [@b107-gmb-35-2-365] studied 63 binary polymorphisms and 10 STR regions in 2,344 persons from 15 Northern and three Southern Amerindian groups. Only a few recent studies have used all known SNPs necessary to identify the major Native American Y-haplogroups and their sublineages in Amerindian populations ([@b40-gmb-35-2-365]; [@b46-gmb-35-2-365]; [@b11-gmb-35-2-365]).

The most recent mtDNA reviews were published four years ago and involved sequence variability in the hypervariable region 1 ([@b44-gmb-35-2-365]; [@b55-gmb-35-2-365]). [@b83-gmb-35-2-365], on the other hand, associated data from Y-chromosome markers with mitochondrial DNA (mtDNA) results, providing a good picture of the information available at the time. No general review considering both data sets has been published since then.

This review provides a detailed, comprehensive survey of Y-chromosome haplogroup frequency variation in 68 populations involving 1,814 individuals. In addition, specific information on Y-STR markers for 29 populations and 590 subjects is given. The haplogroup mtDNA data included 108 populations involving a total of 6,697 persons. Geographic and linguistic factors that may have influenced this variation were carefully considered, leading to a global, overview of the genetic pattern associated with these markers in South Amerindians. Information on mtDNA sequencing studies is also supplied.

Materials and Methods
=====================

The data used in this review were obtained from 17 primary surveys of the Y-chromosome and 66 primary surveys of mtDNA. These studies were retrieved through PubMed and by searching the reference lists of the corresponding papers. Haplogroup frequencies were obtained by direct counting. Intra- and inter-populational diversity was calculated with AMOVA ([@b104-gmb-35-2-365]; [@b31-gmb-35-2-365]; [@b103-gmb-35-2-365]) using Arlequin 3.5.1.2 software ([@b30-gmb-35-2-365]). AMOVA was also used to estimate the level of differentiation between and within 17 pre-defined language and 7 geographical categories, respectively. The distribution patterns of the mtDNA haplogroup frequencies were established by generating isoline maps using IDRISI 16.0 software (IDRISI Taiga) ([@b28-gmb-35-2-365]). Spearman's correlation coefficients were calculated with PASW Statistics 18 software. Average heterozygosity (ah) was calculated with Arlequin 3.5.1.2 software.

Results and Discussion
======================

[Table 1](#t1-gmb-35-2-365){ref-type="table"} gives the distribution of the Q and non-Q-chromosomes (defined by a set of SNPs), as well as linguistic and geographical information for the samples considered. The samples were distributed from latitude 11° North to 45° South and longitude 46° to 76° West, with the individuals involved speaking 23 languages. Sample sizes varied widely from 1 to 151 individuals. Twenty-two of the studies involved less than 10 persons. Unfortunately, there is no standardization on the number of SNPs studied and in most cases only the M242 and M3 markers (which define the Asian/Native American paragroup Q\* and its autochthonous Native American sublineage Q1a3a\*, respectively; [@b70-gmb-35-2-365]; [@b16-gmb-35-2-365]; [@b85-gmb-35-2-365]) were investigated. This fact precludes a complete, precise view of the distribution of Q1a3a sublineages and other Q clade chromosomes in South America. For this reason, the information in [Table 1](#t1-gmb-35-2-365){ref-type="table"} was limited to the frequencies of the Q and non-Q-lineages only. Note that non-Q-chromosomes (which, for the reasons given above, could not be identified in sublineages) were identified in ∼50% of the tribal groups. For some of these populations admixture with non-Indians is known and could be the source of these non-Q chromosomes (for example, Mapuche and Guarani; [@b57-gmb-35-2-365]; [@b5-gmb-35-2-365]; [@b12-gmb-35-2-365]). Overall, the numbers presented in [Table 1](#t1-gmb-35-2-365){ref-type="table"} indicate a higher presence of non-Q lineages in southern populations than in those of the northern/Amazonian region, probably because of greater admixture with non-Indians in the former than in the latter. However, for some isolated groups such as the Yanomámi, it is unlikely that admixture explains the findings. In these cases other causes are more probable, such as the presence of unknown autochthonous lineages and/or known Q lineages whose defining markers were not tested.

Despite the great variation in the number of Y-SNPs used in these studies, [Figure 1](#f1-gmb-35-2-365){ref-type="fig"} illustrates some of the trends that were observed: The autochthonous Native American Q1a3a\* is almost always the most prevalent, whereas its sublineages (Q1a3a1, Q1a3a2, Q1a3a3 and Q1a3a4) seem to have more restricted geographical distributions. The second most prevalent, Q1a3\*, appears to occur equally in all regions, suggesting its presence among the first settlers of South America. The other known Q clade chromosomes (Q1\*, Q1a\*, Q1a1, Q1a2, Q1a4, Q1a5, Q1a6 and Q1b) have not yet been identified in South America. Only one non-Q-chromosome (C3\*) of probable native origin has been described in northwest South Amerindian populations ([Figure 1](#f1-gmb-35-2-365){ref-type="fig"}; [@b40-gmb-35-2-365]).

The nature of some evolutionary and demographic scenarios, mediated by men, in native American populations has also been evaluated by using Y microsatellite markers (Y-STRs), which have a much faster evolutionary rate than SNPs. Y-STRs allow the retrieval of population and chromosome evolutionary histories. For example, STR data have been used to estimate that the mutations that gave rise to the Q1a3a1 and Q1a3a4 sublineages occurred 7,972 ± 2,916 and 5,280 ± 1,330 years ago, probably in northwest South America and the Andean region, respectively ([@b16-gmb-35-2-365]; [@b46-gmb-35-2-365]).

[Table 2](#t2a-gmb-35-2-365){ref-type="table"} shows the STR allele frequencies observed in 29 South Amerindian populations, based only on Q clade chromosomes. In this compilation, we considered only studies containing information on the allele frequencies for each population individually. There was considerable variation in the number of samples tested in each study, the number of tribes, and the number of individuals per tribe. Depending on the locus considered, the number of alleles observed ranged from one to eight, with some of them appearing in only one study while others were present in almost all populations. Based on the most prevalent alleles per locus we reconstructed a probable haplotype of the ancient Native American Q-clade chromosome (ANAQC) as: 13(DYS19)-12(DYS388)-14(DYS389I)-31(DYS389II)-2 4(DYS390)-10(DYS391)-14(DYS392)-13(DYS393)-14(DYS437)-11(DYS438)-12(DYS439)-20(DYS448)-15(D YS456)-16(DYS458)-22(DYS635). Using this information and additional data for these loci (except DYS388) reported in the Y Chromosome Haplotype Reference Database we found no matches in 36,448 haplotypes (245 populations). Although we found no complete identity with our estimated ANAQC, three one-step neighbor haplotypes were encountered, two in individuals with an admixed ancestry living in Latin American countries and one in a Native American individual (Kaqchiquel).

[Table 3](#t3-gmb-35-2-365){ref-type="table"} shows the results of the molecular analysis of variance for populations structured by language or geography based on the data in [Table 2](#t2a-gmb-35-2-365){ref-type="table"}. The estimates were calculated for each STR locus because testing heterogeneity prevented haplotype identification. As expected, most of the diversity was attributable to intrapopulation variation, with one exception (DYS437) that was explained by the fixation of allele 14 in 40% of the populations, whereas only allele 8 was found in the Wichí. In contrast, significant variation among subdivisions was detected for only six loci (DYS398I, DYS391, DYS392, DYS393, DYS437 and DYS456) and in five out of these six it was attributable to geography. There was also considerable inter-population/within subdivision variability (significant in 28 of 30 evaluations), with the average percentage being 16% for geography and 21% for language.

[Table 4](#t4-gmb-35-2-365){ref-type="table"} summarizes the information on sequencing studies of mitochondrial DNA. The mtDNA genome of representative individuals from 35 populations has been entirely sequenced, as reported in six publications ([@b45-gmb-35-2-365]; [@b51-gmb-35-2-365]; [@b90-gmb-35-2-365]; [@b32-gmb-35-2-365]; [@b71-gmb-35-2-365], [@b72-gmb-35-2-365]). However, the analyses performed did not consider the within South Amerindian relationships and were mostly concerned with interethnic or interhaplogroup comparisons. Based on 86 complete Amerindian genomes, [@b32-gmb-35-2-365] concluded that the prehistoric colonization of the Americas involved a single founding population, with an initial differentiation from Asia occurring in Beringia that ended around 19,000--23,000 years ago, with a moderate bottleneck. Expansion into the New World would have occurred about 18,000 years ago. An extensive 5.76 kb analysis by [@b27-gmb-35-2-365] established that haplogroup X is not present in extant South American Indians.

The most extensive set of data involves the highly variable segment 1 (HVS-I) that has been studied in 92 populations and reported in 30 papers; surveys that have included the HVS-II region are much less common (10 articles) ([Table 4](#t4-gmb-35-2-365){ref-type="table"}). For HVS-I, [@b64-gmb-35-2-365] provided an excellent example of how intrapopulation variability in the Yanomámi could be interpreted in a historical and demographical context and relating it to other Amerindian and Asian data. They studied 129 Yanomámi sequences from individuals in eight villages and compared their haplotypes with those of other Asian and New World populations, in a total of 482 unique haplotypes. Interestingly, the pairwise inter-population gene flow estimates were lower between some pairs of Yanomámi villages than between them and four other South Amerindian groups.

With regard to intrapopulation variability, as measured by Θ~k~, [@b35-gmb-35-2-365] and [@b21-gmb-35-2-365] reported extensive variation for 14 and 27 Central and Southern Amerindian populations, respectively (*e.g.*, from 0.659 for the Quechua of Peru to 0.011 for the Xavante of the Brazilian Mato Grosso). Intra- and intergroup nucleotide diversity was calculated by [@b59-gmb-35-2-365] for 20 of these Amerindian groups, whereas [@b6-gmb-35-2-365] compared the sources of variation among North, Central and South Amerindians in 51 populations; the latter authors observed 3% variation among the three sets, 21% variation among populations within the subcontinent and 76% variation within populations.

To explore the mtDNA data further we compiled the prevalences of haplogroups A--D for 109 populations, in a total of 6,697 individuals distributed between latitude 11° North and 54° South, and longitude 46° to 78° West ([Table 5](#t5-gmb-35-2-365){ref-type="table"}). Sample sizes varied widely, from only one subject tested (Jebero) up to 491 (Yanomámi). The haplogroup frequencies reported in 52 articles also varied widely. The presence of mtDNA genomes of probable non-Amerindian origin was rare in all regions and populations, in contrast to the Y-SNP data ([Table 1](#t1-gmb-35-2-365){ref-type="table"}). Asymmetrical sex-mediated admixture was common during the first centuries of South American colonization, and involved mostly European men and Amerindian/African women. The main consequences of this historical contact was the formation of mestizos and the present-day national societies; the former are characterized by a composite genome, with the majority of Y-chromosomes being of European origin, while their mtDNA derives from Amerindian or African sources ([@b14-gmb-35-2-365]; [@b3-gmb-35-2-365]; [@b20-gmb-35-2-365]; [@b79-gmb-35-2-365]). Asymmetrical mating could also explain the introduction of non-Amerindian Y-chromosomes into the tribes, while the autochthonous mtDNA genomes were preserved. However, the admixture dynamics are probably different from those observed in urban groups since they normally involve Amerindian women who live on reservations and men who live near the border of the reservations. In this situation, the children normally remain with their mothers. This phenomenon has been described for Guarani Indians ([@b57-gmb-35-2-365]), but the data presented here indicate that it could be much more common than previously thought.

[Table 6](#t6-gmb-35-2-365){ref-type="table"} summarizes the influence of geography. In the seven regions that were defined, 74% of the variation occurred within populations, 6% among geographic divisions and 20% among populations within divisions. To analyze this variability further, the isolated frequencies of haplogroups A to D were plotted as shown in [Figure 2](#f2-gmb-35-2-365){ref-type="fig"}. High frequencies of haplogroup C were observed in specific regions along the northwestern portion of the continent, with additional high spots in southern Brazil and northern Argentina. The prevalences of haplogroups B and D showed a clear east-west separation, while for haplo-group A there were three main high prevalence nuclei in the north, center and south of the continent. Spearman's correlation coefficient between haplogroup frequencies and latitude yielded a positive value (0.27; p \< 0.01) for haplogroup A, with a corresponding negative one (−0.25; p \< 0.01) for haplogroup D. The coefficients for haplo-groups B and C were not significant.

[Table 7](#t7-gmb-35-2-365){ref-type="table"} summarizes the influence of language. Sixteen main language groups were considered, plus a composite set of "others". The AMOVA results indicated that 73% of the haplogroup prevalence variability occurred within populations, with 7% of it being attributable to languages. However, there was considerable heterogeneity (20%) within the language categories established. Overall, the variability was similar to that obtained for geography.

Conclusion
==========

South Amerindians have been extensively studied with regard to the Y-chromosome, as well as and especially so for mtDNA markers. In agreement with studies from other regions, by far most of the mtDNA variability (73%--74%) is intrapopulational. Geographical and linguistic factors influenced the patterns of mtDNA diversity to a similar extent, while geography was apparently more important than language in explaining the data for the Y chromosome Q clade-STRs. Additional factors that may have influenced these results include distinct male and female migration patterns, as well as cultural and other characteristics. The fact that most studies have generally dealt with small populations, in which genetic drift may be important, could also have influenced the results.

This work was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul, Programa de Apoio a Núcleos de Excelência (FAPERGS/PRONEX). We thank Sidia M. Callegari-Jacques and Luciana Tovo-Rodrigues for their help with early aspects of the statistical analyses.

Associate Editor: Mara H. Hutz

![Y-chromosome phylogenetic tree considering only the Q derived lineages. Note: The letters and numbers in the branches indicate the name of the loci where the mutations occurred, leading to the haplogroup classification. The data for this tree were compiled from the references in [Table 1](#t1-gmb-35-2-365){ref-type="table"}, plus [@b80-gmb-35-2-365], [@b98-gmb-35-2-365], [@b99-gmb-35-2-365]), Karafet *et al.* ([@b47-gmb-35-2-365], [@b48-gmb-35-2-365], [@b49-gmb-35-2-365]), [@b19-gmb-35-2-365], [@b100-gmb-35-2-365], [@b15-gmb-35-2-365], The [@b91-gmb-35-2-365] and [@b40-gmb-35-2-365].](gmb-35-2-365-gfig1){#f1-gmb-35-2-365}

![Isoline map distribution showing the geographic pattern of the four (A--D) mtDNA haplogroups in South Amerindians. The dots indicate the locations of the populations sampled. As indicated in the scales given at right of each map, the colors represent the haplogroup frequencies, from dark blue (0.00) to red (1.00).](gmb-35-2-365-gfig2){#f2-gmb-35-2-365}

###### 

The distribution of Q and non-Q lineages and linguistic and geographical information for the samples considered.

  Populations (n)[^1^](#tfn1-gmb-35-2-365){ref-type="table-fn"}   Haplogroup (%)   Language[^2^](#tfn2-gmb-35-2-365){ref-type="table-fn"}   Geographical coordinates                                 References                               
  --------------------------------------------------------------- ---------------- -------------------------------------------------------- -------------------------------------------------------- ---------------------------------------- ---------------------------------------------------------------
  Wayuu (19)                                                      69               31                                                       Arawakan                                                 11° N; 73° W                             [@b16-gmb-35-2-365]
  Kogi (17)                                                       100                                                                       Chibchan                                                 11° N; 74° W                             [@b76-gmb-35-2-365]
  Barira (12)                                                     100                                                                       Chibchan                                                 10° 44′ N; 71° 23′ W                     [@b16-gmb-35-2-365]
  Arsario (Wiwa) (6)                                              100                                                                       Chibchan                                                 10° 25′ N; 73° 05′ W                     [@b76-gmb-35-2-365]
  Arhuaco (Ijka) (19)                                             100                                                                       Chibchan                                                 9° 04′ N; 73° 59′ W                      [@b76-gmb-35-2-365]
  Warao (12)                                                      100                                                                       Warao                                                    9° N; 61° W                              [@b16-gmb-35-2-365]
  Yukpa (12)                                                      100                                                                       Carib                                                    8° 40′ N; 72° 41′ W                      [@b16-gmb-35-2-365]
  Zenu (52)                                                       79               21                                                       Spanish[^3^](#tfn3-gmb-35-2-365){ref-type="table-fn"}    8° 30′ N; 76° W                          [@b16-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Embera (13)                                                     92               8                                                        Choco                                                    7° N; 76° 30′ W                          [@b76-gmb-35-2-365]
  Makiritare (25)                                                 68               32                                                       Carib                                                    5° 33′ N; 65° 33′ W                      [@b53-gmb-35-2-365]
  Kali'na (21)                                                    81               19                                                       Carib                                                    5° 31′ N; 53° 47′ W                      [@b58-gmb-35-2-365]
  Waunana (29)                                                    100                                                                       Choco                                                    4° 50′ N; 77° W                          [@b76-gmb-35-2-365]
  Palikur (35)                                                    94               6                                                        Arawakan                                                 4° N; 51° 45′ W                          [@b58-gmb-35-2-365]
  Macushi (4)                                                     100                                                                       Carib                                                    4° N; 60° 50′ W                          [@b53-gmb-35-2-365]
  Piaroa (6)                                                      100                                                                       Salivan                                                  3° 57′ N; 66° 22′ W                      [@b53-gmb-35-2-365]
  Wapishana (2)                                                   50               50                                                       Arawakan                                                 3° 07′ N; 60° 03′ W                      [@b53-gmb-35-2-365]
  Emerillon (9)                                                   100                                                                       Tupi                                                     3° N; 53° W                              [@b58-gmb-35-2-365]
  Yanomámi (39)                                                   38               62                                                       Yanomam                                                  2° 50′ N; 54° W                          [@b75-gmb-35-2-365]; [@b53-gmb-35-2-365]
  Tiryió (4)                                                      100                                                                       Carib                                                    2° N; 56° W                              [@b16-gmb-35-2-365]
  Apalaí (57)                                                     98               2                                                        Carib                                                    1° 20′ N; 54° 40′ W                      [@b75-gmb-35-2-365]; [@b16-gmb-35-2-365]
  Wayampi (62)                                                    100                                                                       Tupi                                                     1° N; 53° W                              [@b75-gmb-35-2-365]; [@b16-gmb-35-2-365]; [@b58-gmb-35-2-365]
  Yagua (7)                                                       100                                                                       Peba-Yaguan                                              0° 51′ N; 72° 27′ W                      [@b16-gmb-35-2-365]
  Ingano (108)                                                    80               20                                                       Quechuan                                                 0° 50′ N; 77° W                          [@b16-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Wai-Wai (9)                                                     100                                                                       Carib                                                    0° 40′ S; 58° W                          [@b11-gmb-35-2-365]
  Urubu-Kaapor (16)                                               100                                                                       Tupi                                                     2°--3° S; 46°--47° W                     [@b16-gmb-35-2-365]
  Huitoto (4)                                                     75               25                                                       Witotoan                                                 2° 14′ S; 72° 19′ W                      [@b16-gmb-35-2-365]
  Arara (15)                                                      100                                                                       Carib                                                    3° 30′--4° 20′ S; 53° 0′--54° 10′ W      [@b75-gmb-35-2-365]; [@b10-gmb-35-2-365]; [@b11-gmb-35-2-365]
  Asurini (4)                                                     100                                                                       Tupi                                                     3° 35′--4° 12′ S; 49° 40′--52° 26′ W     [@b16-gmb-35-2-365]
  Ticuna (59)                                                     93               7                                                        Ticuna                                                   4° S; 69° 58′ W;                         [@b16-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Parakanã (20)                                                   100                                                                       Tupi                                                     5° 22′ S; 51° 17′ W                      [@b16-gmb-35-2-365]
  Xikrin (14)                                                     100                                                                       Macro-Ge                                                 5° 55′ S; 51° W                          [@b16-gmb-35-2-365]; [@b11-gmb-35-2-365]
  Suruí (24)                                                      96               4                                                        Tupi                                                     5° 58′--10° 50′ S; 48° 39′--61° 10′ W    [@b97-gmb-35-2-365]; [@b11-gmb-35-2-365]
  Araweté (4)                                                     100                                                                       Tupi                                                     5° 9′ S; 52° 22′ W                       [@b11-gmb-35-2-365]
  Munduruku (1)                                                   100                                                                       Tupi                                                     6° 23′ S; 59° 9′ W                       [@b11-gmb-35-2-365]
  Jamamadi (3)                                                    100                                                                       Arauan                                                   7° 15′ S; 66° 41′ W                      [@b11-gmb-35-2-365]
  Gorotire (19)                                                   100                                                                       Macro-Ge                                                 7° 44′ S; 51° 10′ W                      [@b16-gmb-35-2-365]; [@b11-gmb-35-2-365]
  Krahó (15)                                                      93               7                                                        Macro-Ge                                                 8° S; 47° 15′ W                          [@b53-gmb-35-2-365]; [@b16-gmb-35-2-365]
  Kuben-Kran-Kegn (9)                                             100                                                                       Macro-Ge                                                 8° 10′ S; 52° 8′ W                       [@b11-gmb-35-2-365]
  Tenharim (1)                                                    100                                                                       Tupi                                                     8° 20′ S; 62° W                          [@b11-gmb-35-2-365]
  Mekranoti (9)                                                   78               22                                                       Macro-Ge                                                 8° 40′ S; 54° W                          [@b16-gmb-35-2-365]
  Kayapó (10)                                                     100                                                                       Macro-Ge                                                 9° S; 53° W                              [@b75-gmb-35-2-365]
  Karitiana (18)                                                  100                                                                       Tupi                                                     9° 30′ S; 64° 15′ W                      [@b97-gmb-35-2-365]; [@b11-gmb-35-2-365]
  Cinta-Larga (15)                                                100                                                                       Tupi                                                     9° 50′--12° 30′ S; 59° 10′--60° 50′ W    [@b16-gmb-35-2-365]
  Gavião (7)                                                      100                                                                       Tupi                                                     10° 10′ S; 61° 8′ W                      [@b11-gmb-35-2-365]
  Karipuna (1)                                                                     100                                                      Tupi                                                     10° 14′ S; 64° 13′ W                     [@b11-gmb-35-2-365]
  Zoró (6)                                                        100                                                                       Tupi                                                     10° 20′ S; 60° 20′ W                     [@b11-gmb-35-2-365]
  Matsiguenga (28)                                                91               9                                                        Arawakan                                                 10° 47′--12° 51′ S; 73° 17′ -70° 44′ W   [@b58-gmb-35-2-365]
  Pacaás Novos (Wari) (29)                                        100                                                                       Chapacura-Wanham                                         11° 8′ S; 65° W                          [@b16-gmb-35-2-365]
  Panoa (5)                                                       100                                                                       Pano                                                     12° 55′ S; 65° 12′ W                     [@b53-gmb-35-2-365]
  Xavante (15)                                                    100                                                                       Macro-Ge                                                 14° S; 52° 30′ W                         [@b11-gmb-35-2-365]
  Quechua (44)                                                    73               27                                                       Quechuan                                                 14° 30′ S; 69° W                         [@b39-gmb-35-2-365]
  Aymara (59)                                                     97               3                                                        Aymaran                                                  17° 68′ S; 69° 16′ W                     [@b39-gmb-35-2-365]
  Ayoreo (9)                                                      78               22                                                       Zamucoan                                                 19° S; 60° 30′ W                         [@b5-gmb-35-2-365]
  Wichí (Mataco) (151)                                            48               52                                                       Mataco-Guaicuru                                          22° 28′ S; 62° 70′ W                     [@b23-gmb-35-2-365]; [@b5-gmb-35-2-365]
  Lengua (36)                                                     97               3                                                        Mascoian                                                 22° 45′ S; 58° 5′ W                      [@b5-gmb-35-2-365]; [@b11-gmb-35-2-365]
  Chorote (9)                                                     89               21                                                       Mataco-Guaicuru                                          22° 90′ S; 65° 40′ W;                    [@b5-gmb-35-2-365]
  Aché (54)                                                       98               2                                                        Tupi                                                     23° 30′--24° 10′ S; 55° 50′--56° 30′ W   [@b16-gmb-35-2-365]
  Guarani (78)                                                    77               23                                                       Tupi                                                     23° 6′ S; 55° 12′ W                      [@b16-gmb-35-2-365]; [@b57-gmb-35-2-365]
  Pilagá                                                          47               53                                                       Mataco-Guaicuru                                          24° S; 59° W                             [@b23-gmb-35-2-365]
  Colla (63)                                                      35               65                                                       Quechuan[^3^](#tfn3-gmb-35-2-365){ref-type="table-fn"}   24° 10′--24° 43′ S; 65° 17′--65° 52′ W   [@b12-gmb-35-2-365]; [@b96-gmb-35-2-365]
  Toba (89)                                                       88               12                                                       Mataco-Guaicuru                                          26° S; 58° W                             [@b23-gmb-35-2-365]; [@b5-gmb-35-2-365]; [@b96-gmb-35-2-365]
  Kaingang (59)                                                   69               31                                                       Macro-Ge                                                 28° S; 51° 20′ W                         [@b16-gmb-35-2-365]; [@b57-gmb-35-2-365]; [@b11-gmb-35-2-365]
  Diaguita (24)                                                   37               63                                                       Quechuan[^4^](#tfn4-gmb-35-2-365){ref-type="table-fn"}   28° 20′ S; 67° 43′ W                     [@b12-gmb-35-2-365]
  Mocoví (40)                                                     60               40                                                       Mataco-Guaicuru                                          29° 51′ S; 59° 56′ W                     [@b5-gmb-35-2-365]
  Pehuenche (18)                                                  83               17                                                       Araucanian                                               37° 43′ S; 71° 16′ W                     [@b5-gmb-35-2-365]
  Mapuche (105)                                                   36               64                                                       Araucanian                                               39° 10′--41° 20′ S; 68° 37′--70° 22′ W   [@b5-gmb-35-2-365]; [@b12-gmb-35-2-365]
  Huilliche (26)                                                  50               50                                                       Araucanian                                               41° 16′ S; 73° W                         [@b5-gmb-35-2-365]
  Tehuelche (20)                                                  65               35                                                       Chon                                                     45° S; 71° W                             [@b5-gmb-35-2-365]

Arranged according to latitude.

Classification according to [@b109-gmb-35-2-365].

Original language is extinct.

The Diaguita spoke originally Kakán, but this language became extinct and was substituted by Quechua.

###### 

Y-Q-chromosome STR studies in distinct South Amerindian samples in which allele frequencies can be assessed (Part A).

                   Ref. (n)                                                                                                           
  ---------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- -------
  DYS19 (12)                                  0.020                                   0.250                                           
  DYS19 (13)       1.000                      0.820           0.920   1.000   0.790   0.620   0.300           0.910   0.500   0.830   0.600
  DYS19 (14)                                  0.160   1.000   0.080           0.190   0.130   0.300           0.090   0.330   0.040   0.400
  DYS19 (15)                                                                  0.020           0.350                   0.170   0.130   
  DYS19 (16)                                                                                  0.050                                   
  DYS19 total                                                                                                                         
  DYS388 (12)      1.000                                      1.000                   0.750                                           1.000
  DYS388 (13)                                                                         0.120                                           
  DYS388 (14)                                                                         0.130                                           
  DYS388 (17)                                                                                                                         
  DYS388 total                                                                                                                        
  DYS389I (12)                                0.020                           0.280           0.180           0.040   0.160   0.040   
  DYS389I (13)                                0.470   0.500           0.220   0.020           0.820           0.410   0.500   0.750   
  DYS389I (14)                                0.510   0.500           0.780   0.550                           0.550   0.170   0.210   
  DYS389I (15)                                                                0.150                                   0.170           
  DYS389I total                                                                                                                       
  DYS389II (17)                                                                                                                       
  DYS389II (18)                                                                                                                       
  DYS389II (19)                                                                                                                       
  DYS389II (26)                                                                               0.060                                   
  DYS389II (27)                                                                                                       0.160           
  DYS389II (28)                               0.020                           0.020           0.120                                   
  DYS389II (29)                               0.090   0.500                   0.150           0.290           0.090   0.500   0.290   
  DYS389II (30)                               0.370   0.500           0.440   0.130           0.470           0.180   0.170   0.420   
  DYS389II (31)                               0.450                   0.560   0.620           0.060           0.500           0.250   
  DYS389II (32)                               0.070                           0.080                           0.090   0.170   0.040   
  DYS389II (33)                                                                                               0.140                   
  DYS389II (34)                                                                                                                       
  DYS389II total                                                                                                                      
  DYS390 (20)                                                                                                                         
  DYS390 (21)                 0.230   0.120   0.070                                           0.060   0.100   0.040                   
  DYS390 (22)                 0.110                                           0.130                                           0.040   
  DYS390 (23)      1.000      0.330   0.880   0.560           0.080   0.330   0.080   0.250           0.100   0.640   0.330   0.420   0.400
  DYS390 (24)                 0.330           0.250   1.000   0.920   0.450   0.680   0.370   0.940   0.700   0.180   0.670   0.330   0.600
  DYS390 (25)                                 0.120                   0.220   0.090   0.250           0.100                   0.210   
  DYS390 (26)                                                                 0.020   0.130                   0.140                   
  DYS390 (27)                                                                                                                         
  DYS390 total                                                                                                                        
  DYS391 (9)                                  0.020                                                                           0.210   
  DYS391 (10)      1.000                      0.820   1.000   1.000   0.890   0.210   0.860                   0.820   1.000   0.750   1.000
  DYS391 (11)                                 0.140                   0.110   0.790   0.140                   0.180           0.040   
  DYS391 (12)                                 0.020                                                                                   
  DYS391 total                                                                                                                        
  DYS392 (11)                                                                                 0.060                                   
  DYS392 (12)                                                                                                 0.140                   
  DYS392 (13)                 1.000   1.000                   0.920           0.070   0.120   0.350   0.700   0.050           0.170   1.000
  DYS392 (14)      1.000                      0.470   0.500   0.080   0.450   0.720   0.880   0.530   0.300   0.360   0.830   0.710   
  DYS392 (15)                                 0.040   0.500           0.330   0.210           0.060           0.090   0.170   0.120   
  DYS392 (16)                                 0.470                   0.220                                   0.360                   
  DYS392 (17)                                 0.020                                                                                   
  DYS392 (18)                                                                                                                         
  DYS392 total                                                                                                                        
  DYS393 (11)                                                                 0.480                                                   
  DYS393 (12)                 0.220   0.120                   0.080           0.090   0.120   0.060   0.400   0.090                   0.400
  DYS393 (13)      1.000      0.780   0.880   0.440   1.000           0.670   0.340   0.760   0.590   0.600   0.550   1.000   1.000   0.600
  DYS393 (14)                                 0.560           0.920   0.330   0.090   0.120   0.350           0.360                   
  DYS393 (15)                                                                                                                         
  DYS393 (16)                                                                                                                         
  DYS393 total                                                                                                                        
  DYS437 (8)                                                                                                                          
  DYS437 (9)                                                                                                                          
  DYS437 (11)                                                                                                                 0.040   
  DYS437 (14)                                 1.000                   1.000   0.930           0.590           1.000           0.920   
  DYS437 (15)                                                                 0.070           0.410                           0.040   
  DYS437 total                                                                                                                        
  DYS438 (9)                                                                                                                          
  DYS438 (10)                                 0.050                   0.220                                                   0.040   
  DYS438 (11)                                 0.930                   0.670   0.860           0.590           1.000           0.920   
  DYS438 (12)                                 0.020                   0.110   0.140           0.410                                   
  DYS438 (16)                                                                                                                 0.040   
  DYS438 total                                                                                                                        
  DYS439 (9)                                                                                                  0.050                   
  DYS439 (10)                                                                                 0.060                           0.130   
  DYS439 (11)                                 0.160                   0.220   0.070           0.230           0.050           0.220   
  DYS439 (12)                                 0.240                   0.450   0.640           0.590           0.360           0.390   
  DYS439 (13)                                 0.370                   0.330   0.290           0.060           0.270           0.260   
  DYS439 (14)                                 0.230                                           0.060           0.270                   
  DYS439 total                                                                                                0.200                   
  DYS448 (18)                                                                                                                         
  DYS448 (19)                                 0.110                                                                                   
  DYS448 (20)                                 0.770                                                           0.800                   
  DYS448 (21)                                 0.120                                                                                   
  DYS448 (22)                                                                                                                         
  DYS448 total                                                                                                                        
  DYS456 (11)                                 0.020                                                                                   
  DYS456 (13)                                 0.050                                                                                   
  DYS456 (14)                                 0.020                                                                                   
  DYS456 (15)                                 0.800                                                           0.900                   
  DYS456 (16)                                 0.090                                                           0.100                   
  DYS456 (17)                                 0.020                                                                                   
  DYS456 total                                                                                                                        
  DYS458 (13)                                 0.050                                                           0.100                   
  DYS458 (15)                                 0.030                                                                                   
  DYS458 (16)                                 0.490                                                           0.700                   
  DYS458 (17)                                 0.250                                                           0.200                   
  DYS458 (18)                                 0.140                                                                                   
  DYS458 (19)                                 0.040                                                                                   
  DYS458 total                                                                                                                        
  DYS635 (22)                                 0.820                                                           0.700                   
  DYS635 (23)                                 0.160                                                           0.300                   
  DYS635 (24)                                                                                                                         
  DYS635 (26)                                 0.020                                                                                   
  DYS635 total                                                                                                                        

[@b75-gmb-35-2-365];

[@b16-gmb-35-2-365];

[@b23-gmb-35-2-365];

[@b1-gmb-35-2-365];

[@b52-gmb-35-2-365];

[@b95-gmb-35-2-365];

[@b5-gmb-35-2-365];

[@b12-gmb-35-2-365];

[@b39-gmb-35-2-365];

[@b46-gmb-35-2-365].

###### 

Y-Q-chromosome STR studies in distinct South Amerindian samples in which allele frequencies can be assessed (Part B).

                   Ref. (n)                                                                                                           
  ---------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- ------- -------
  DYS19 (12)                                                          0.030                           0.030                           0.010
  DYS19 (13)       0.500                      0.790   0.950   0.850   0.870   1.000           0.790   0.640           0.550   0.650   0.890
  DYS19 (14)       0.500      1.000           0.210   0.030   0.090   0.090                   0.140   0.230           0.450   0.270   0.050
  DYS19 (15)                                          0.020   0.060   0.010                   0.070   0.100                   0.080   0.040
  DYS19 (16)                                                                                                                          0.010
  DYS19 total                                                                                                                         474
  DYS388 (12)                 0.860   1.000                   0.780           0.750           0.570                   0.500   0.500   0.780
  DYS388 (13)                 0.140                           0.220           0.250           0.430                   0.500   0.430   0.200
  DYS388 (14)                                                                                                                         0.010
  DYS388 (17)                                                                                                                 0.070   0.040
  DYS388 total                                                                                                                        189
  DYS389I (12)                                        0.090                                                                           0.080
  DYS389I (13)     1.000                              0.240           0.800                                                           0.440
  DYS389I (14)                                        0.670           0.200                                                           0.450
  DYS389I (15)                                                                                                                        0.030
  DYS389I total                                                                                                                       288
  DYS389II (17)                                       0.270                                                                           0.020
  DYS389II (18)                                       0.530                                                                           0.030
  DYS389II (19)                                       0.200                                                                           0.010
  DYS389II (26)                                                                                                                       0.010
  DYS389II (27)                                                                                                                       0.010
  DYS389II (28)                                       0.090                                                                           0.030
  DYS389II (29)                                       0.070                                                                           0.110
  DYS389II (30)                                       0.210           0.500                                                           0.290
  DYS389II (31)    0.500                              0.540           0.320                                                           0.390
  DYS389II (32)    0.500                              0.090           0.160                                                           0.080
  DYS389II (33)                                                                                                                       0.010
  DYS389II (34)                                                       0.020                                                           0.010
  DYS389II total                                                                                                                      288
  DYS390 (20)                                         0.020                                                                           0.010
  DYS390 (21)                                         0.240                                                                           0.070
  DYS390 (22)                                         0.020           0.080                           0.030   0.780                   0.070
  DYS390 (23)      0.500      0.450           0.210   0.450   0.060   0.110   0.080   1.000   0.220   0.070                   0.250   0.320
  DYS390 (24)      0.500      0.550   1.000   0.790   0.220   0.150   0.730   0.920           0.560   0.740   0.110   1.000   0.290   0.400
  DYS390 (25)                                         0.050   0.760   0.080                   0.220   0.130                   0.420   0.110
  DYS390 (26)                                                                                         0.030                           0.010
  DYS390 (27)                                                 0.030                                           0.110           0.040   0.010
  DYS390 total                                                                                                                        659
  DYS391 (9)                                                                                  0.070   0.030                           0.030
  DYS391 (10)      1.000      1.000           0.890   0.840   0.930   0.900   0.250           0.570   0.870           1.000   0.640   0.800
  DYS391 (11)                         1.000   0.110   0.160   0.070   0.100   0.750           0.360   0.100                   0.360   0.160
  DYS391 (12)                                                                                                                         0.010
  DYS391 total                                                                                                                        512
  DYS392 (11)                                                         0.030                   0.570   0.060                           0.020
  DYS392 (12)                                                                         1.000   0.070                           0.130   0.030
  DYS392 (13)      1.000      0.890           0.100                   0.100   0.110                   0.130   0.890   0.180   0.060   0.170
  DYS392 (14)                 0.110           0.800   0.520   0.380   0.670   0.890           0.290   0.420   0.110   0.460   0.560   0.510
  DYS392 (15)                                 0.100   0.070   0.620   0.190                   0.070   0.390           0.360   0.250   0.150
  DYS392 (16)                                         0.290                                                                           0.100
  DYS392 (17)                                         0.020                                                                           0.010
  DYS392 (18)                                         0.100           0.010                                                           0.010
  DYS392 total                                                                                                                        535
  DYS393 (11)                         1.000                                                                                           0.040
  DYS393 (12)                                                 0.060   0.010                   0.100   0.060                   0.040   0.040
  DYS393 (13)      1.000      0.780           1.000   0.550   0.710   0.980   0.750           0.800   0.840   0.890   0.500   0.200   0.670
  DYS393 (14)                 0.220                   0.450   0.170   0.010   0.250   1.000   0.100   0.100   0.110   0.500   0.240   0.220
  DYS393 (15)                                                 0.030                                                           0.480   0.020
  DYS393 (16)                                                 0.030                                                           0.040   0.010
  DYS393 total                                                                                                                        584
  DYS437 (8)                                  0.420                   0.360                   1.000                                   0.200
  DYS437 (9)                                  0.580                   0.030                                                           0.040
  DYS437 (11)                                                                                                                         0.010
  DYS437 (14)                                         1.000           0.500                                                           0.700
  DYS437 (15)                                                         0.110                                                           0.050
  DYS437 total                                                                                                                        322
  DYS438 (9)                                          0.020                                                                           0.010
  DYS438 (10)                                                         0.050                   0.160                                   0.050
  DYS438 (11)                                 0.790   0.930           0.850                   0.840                                   0.850
  DYS438 (12)                                 0.210   0.050           0.100                                                           0.080
  DYS438 (16)                                                                                                                         0.010
  DYS438 total                                                                                                                        322
  DYS439 (9)                                                                                                                          0.010
  DYS439 (10)                                                                                                                         0.010
  DYS439 (11)                                         0.090           0.130                   0.230                                   0.140
  DYS439 (12)                                 0.320   0.240           0.500                   0.710                                   0.400
  DYS439 (13)                                 0.680   0.500           0.290                   0.060                                   0.330
  DYS439 (14)                                         0.170           0.080                                                           0.110
  DYS439 total                                                                                                                        322
  DYS448 (18)                                                                                                                         0.010
  DYS448 (19)                                         0.140           0.020                                                           0.090
  DYS448 (20)                                         0.550           0.930                                                           0.740
  DYS448 (21)                                         0.240           0.050                                                           0.140
  DYS448 (22)                                         0.070                                                                           0.020
  DYS448 total                                                                                                                        169
  DYS456 (11)                                                                                                                         0.010
  DYS456 (13)                                                                                                                         0.020
  DYS456 (14)                                         0.230           0.020                                                           0.090
  DYS456 (15)                                         0.720           0.730                                                           0.750
  DYS456 (16)                                         0.050           0.250                                                           0.120
  DYS456 (17)                                                                                                                         0.010
  DYS456 total                                                                                                                        169
  DYS458 (13)                                                                                                                         0.020
  DYS458 (15)                                         0.030           0.040                                                           0.040
  DYS458 (16)                                         0.360           0.180                                                           0.380
  DYS458 (17)                                         0.520           0.550                                                           0.410
  DYS458 (18)                                         0.090           0.230                                                           0.140
  DYS458 (19)                                                                                                                         0.010
  DYS458 total                                                                                                                        169
  DYS635 (22)                                         0.950           0.950                                                           0.890
  DYS635 (23)                                         0.020           0.050                                                           0.090
  DYS635 (24)                                         0.030                                                                           0.010
  DYS635 (26)                                                                                                                         0.010
  DYS635 total                                                                                                                        169

[@b75-gmb-35-2-365];

[@b16-gmb-35-2-365];

[@b23-gmb-35-2-365];

[@b1-gmb-35-2-365];

[@b52-gmb-35-2-365];

[@b95-gmb-35-2-365];

[@b5-gmb-35-2-365];

[@b12-gmb-35-2-365];

[@b39-gmb-35-2-365];

[@b46-gmb-35-2-365].

###### 

Analysis of molecular variance of the distinct alleles of the Y-Q STRs in relation to the language and geography of the populations tested.

  STR loci (structured by)                                              Among subdivisions                                    Among populations within subdivisions                 Within populations
  --------------------------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- -----------------------------------------------------
  DYS19 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}       0                                                     0.311[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.689[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS19 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}      0                                                     0.332[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.668[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS388 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0.045                                                 0.317[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.638[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS388 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.091                                                 0.240[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.669[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS389I (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}     0.227[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.030                                                 0.743[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS389I (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}    0.116                                                 0.148[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.736[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS389II (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}    0.036                                                 0.077[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.887[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS389II (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}   0                                                     0.125[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.875[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS390 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0.008                                                 0.326[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.666[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS390 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0                                                     0.359[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.642[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS391 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0                                                     0.385[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.615[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS391 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.253[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.131[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.616[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS392 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0.005                                                 0.319[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.676[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS392 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.007[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.262[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.661[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS393 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0                                                     0.331[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.669[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS393 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.177[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.167[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.656[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS437 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0.289                                                 0.273[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.438[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS437 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.390[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.213[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.397[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS438 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0.048                                                 0.025                                                 0.927[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS438 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.023                                                 0.054[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.923[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS439 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0.019                                                 0.054[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.929[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS439 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.055                                                 0.034[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.911[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS448 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0                                                     0.148[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.852[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS448 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0                                                     0.073[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.927[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS456 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0                                                     0.078[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.922[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS456 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.017[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.044[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.939[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS458 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0                                                     0.144[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.856[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS458 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0.043                                                 0.069[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.888[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS635 (Language)[^1^](#tfn25-gmb-35-2-365){ref-type="table-fn"}      0                                                     0.278[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.722[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}
  DYS635 (Geography)[^2^](#tfn26-gmb-35-2-365){ref-type="table-fn"}     0                                                     0.128[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}   0.872[\*](#tfn27-gmb-35-2-365){ref-type="table-fn"}

Language: Tupi: Aché, Guarani, Parakanã, Wayampi; Carib: Apalaí, Arara, Yukpa; Macro-Ge: Kaingang, Kayapó, Mekranoti; Quechua: Diaguita, Quechua, Ingano; Mataco-Guaicuru: Mocoví, Toba, Wichí, Pilagá; Isolated languages and others with only one population were included as a sixth group.

Geography: Amazonia/Central Brazilian Plateau: Apalaí, Arara, Kayapó, Mekranoti, Pacaás Novos, Parakanã, Ticuna, Warao, Wayampi, Yanomámi; Southern Brazil: Guarani and Kaingang; Chaco: Ache, Ayoreo, Lengua, Mocoví, Pilagá, Toba, Wichí; Andes: Aymara, Barira, Diaguita, Kolla, Quechua, Wayuu, Yukpa, Zenu.

Significant values (p = 0.05). Negative values were adjusted to zero.

###### 

Mitochondrial DNA sequencing studies in South Amerindian populations.

  Population            HVS-I   HVS-II   Complete mt genome   References
  --------------------- ------- -------- -------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  Aché                  X       X        X                    [@b82-gmb-35-2-365]; [@b27-gmb-35-2-365]; [@b32-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Ancash                X                X                    [@b54-gmb-35-2-365]; [@b71-gmb-35-2-365]
  Andean                X                                     [@b38-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Apalaí                X                                     [@b56-gmb-35-2-365]; [@b58-gmb-35-2-365]
  Arara                 X                X                    [@b81-gmb-35-2-365]; [@b56-gmb-35-2-365]; [@b73-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b32-gmb-35-2-365]
  Araweté               X                                     [@b56-gmb-35-2-365]
  Arequipa              X                X                    [@b35-gmb-35-2-365]; [@b71-gmb-35-2-365]
  Arhuaco               X       X        X                    [@b59-gmb-35-2-365]; [@b90-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Arsario               X                X                    [@b59-gmb-35-2-365]; [@b90-gmb-35-2-365]
  Asurini               X       X                             [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]
  Auca                                   X                    [@b51-gmb-35-2-365]
  Awa-Guajá             X                                     [@b81-gmb-35-2-365]; [@b56-gmb-35-2-365]
  Awa-Juriti            X                                     [@b56-gmb-35-2-365]
  Aymara                X       X                             [@b21-gmb-35-2-365]; [@b55-gmb-35-2-365]; [@b106-gmb-35-2-365]; [@b6-gmb-35-2-365]
  Ayoreo                X       X                             Dornelles *et al.* ([@b26-gmb-35-2-365], [@b27-gmb-35-2-365])
  Catamarca                              X                    [@b90-gmb-35-2-365]
  Cayapa                X       X        X                    [@b74-gmb-35-2-365]; [@b90-gmb-35-2-365]
  Chimane               X                                     [@b21-gmb-35-2-365]
  Chilean North Coast   X                                     [@b69-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Cinta Larga           X       X                             [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]
  Coreguaje                              X                    [@b90-gmb-35-2-365]
  Coya                  X       X                             [@b2-gmb-35-2-365]
  Cubeo                 X       X                             [@b92-gmb-35-2-365]
  Curripaco             X       X                             [@b92-gmb-35-2-365]
  Desano                X       X                             [@b92-gmb-35-2-365]
  Diaguita                               X                    [@b72-gmb-35-2-365]
  Embera                X       X        X                    [@b92-gmb-35-2-365]; [@b90-gmb-35-2-365]
  Emerillon             X                                     [@b58-gmb-35-2-365]
  Gavião                X                X                    [@b102-gmb-35-2-365]; [@b32-gmb-35-2-365]
  Gorotire              X       X                             [@b27-gmb-35-2-365]
  Guahibo               X       X                             [@b101-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Guarani               X       X        X                    [@b45-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b27-gmb-35-2-365]; [@b51-gmb-35-2-365]; [@b57-gmb-35-2-365]; [@b32-gmb-35-2-365]; [@b77-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Huilliche             X       X                             [@b106-gmb-35-2-365]
  Huitoto               X       X                             [@b66-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Içana River Indians   X       X                             [@b27-gmb-35-2-365]
  Ignaciano             X                                     [@b8-gmb-35-2-365]
  Inga                  X       X                             [@b92-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Jaqaru                X                                     [@b55-gmb-35-2-365]
  Jamamadi              X                                     [@b56-gmb-35-2-365]
  Jebero                X       X                             [@b66-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Kaingang              X       X                             [@b27-gmb-35-2-365]; [@b57-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Kali'na               X                                     [@b58-gmb-35-2-365]
  Karitiana             X                                     [@b56-gmb-35-2-365];
  Katuena               X                X                    [@b81-gmb-35-2-365]; [@b56-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b32-gmb-35-2-365]
  Kayapó                X                                     [@b56-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}
  Kawéskar              X                                     [@b38-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Kogi                  X       X        X                    [@b59-gmb-35-2-365]; [@b90-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Kolla                                  X                    [@b72-gmb-35-2-365]
  Krahô                 X       X                             [@b27-gmb-35-2-365]
  Kikretun              X                X                    [@b81-gmb-35-2-365]; [@b32-gmb-35-2-365]
  Kubenkokre            X                X                    [@b81-gmb-35-2-365]; [@b32-gmb-35-2-365]
  Kuben-Kran-Kegn       X       X                             [@b27-gmb-35-2-365]
  Lengua                X       X                             [@b27-gmb-35-2-365]
  Mapuche               X       X                             [@b41-gmb-35-2-365]; [@b68-gmb-35-2-365]; [@b27-gmb-35-2-365]
  Mekranoti             X       X                             [@b27-gmb-35-2-365]
  Mocovi                                 X                    [@b90-gmb-35-2-365]
  Movima                X                                     [@b8-gmb-35-2-365]; [@b59-gmb-35-2-365]
  Munduruku             X                                     [@b56-gmb-35-2-365];
  Mura                  X       X                             [@b27-gmb-35-2-365]
  Ocaina                X       X                             [@b66-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Pacaás Novos          X       X                             [@b27-gmb-35-2-365]
  Paez                  X       X                             [@b92-gmb-35-2-365]
  Palikur               X                                     [@b56-gmb-35-2-365]; [@b58-gmb-35-2-365]
  Parakanã              X       X                             [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]
  Pehuenche             X       X                             Merriwether *et al.* ([@b62-gmb-35-2-365], [@b63-gmb-35-2-365]); [@b61-gmb-35-2-365]; [@b67-gmb-35-2-365], [@b68-gmb-35-2-365]); [@b37-gmb-35-2-365]
  Peruvian Andes        X       X                             [@b87-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}; [@b34-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Peruvian Southern     X                                     [@b33-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Coast                                                       
  Piapoco               X       X                             [@b92-gmb-35-2-365]
  Pilagá                X                                     [@b18-gmb-35-2-365]
  Poturujara            X                X                    [@b81-gmb-35-2-365]; [@b56-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b32-gmb-35-2-365]
  Puinave               X       X                             [@b92-gmb-35-2-365]
  Puno                  X                                     [@b55-gmb-35-2-365]
  Quechua               X       X        X                    [@b66-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b35-gmb-35-2-365]; [@b27-gmb-35-2-365]; [@b51-gmb-35-2-365]; [@b21-gmb-35-2-365]; [@b55-gmb-35-2-365]; [@b32-gmb-35-2-365]; [@b106-gmb-35-2-365]; [@b6-gmb-35-2-365]
  Saliva                X       X                             [@b92-gmb-35-2-365]
  Salta                                  X                    [@b90-gmb-35-2-365]
  Sateré Mawé           X       X                             [@b27-gmb-35-2-365]
  Selknam               X                                     [@b38-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Sicán                 X                                     [@b86-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Suruí                 X                X                    [@b56-gmb-35-2-365]; [@b32-gmb-35-2-365]
  Tayacaja              X                                     [@b8-gmb-35-2-365]
  Ticuna                X       X                             [@b66-gmb-35-2-365]; [@b92-gmb-35-2-365]; [@b76-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Tiriyó                X       X        X                    [@b81-gmb-35-2-365]; [@b56-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b27-gmb-35-2-365]; [@b32-gmb-35-2-365]
  Toba                  X                                     [@b18-gmb-35-2-365]
  Trinitario            X                                     [@b8-gmb-35-2-365]
  Tucuman                                X                    [@b90-gmb-35-2-365]
  Tupe                  X                                     [@b55-gmb-35-2-365]
  Txukahamãe            X       X                             [@b27-gmb-35-2-365]
  Uro                   X                                     [@b6-gmb-35-2-365]
  Urubu Kaapor          X       X                             [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]
  Vaupe                                  X                    [@b90-gmb-35-2-365]
  Wai-wai                                X                    [@b32-gmb-35-2-365]
  Wayampi               X       X        X                    [@b81-gmb-35-2-365]; [@b56-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b27-gmb-35-2-365]; [@b32-gmb-35-2-365]; [@b58-gmb-35-2-365]
  Warao                                  X                    [@b45-gmb-35-2-365]
  Waunana                                X                    [@b90-gmb-35-2-365]
  Wayuu                 X       X        X                    [@b92-gmb-35-2-365]; [@b59-gmb-35-2-365]; [@b90-gmb-35-2-365]; [@b106-gmb-35-2-365]
  Wichí                 X                                     [@b18-gmb-35-2-365]
  Xavante               X       X        X                    [@b102-gmb-35-2-365]; [@b27-gmb-35-2-365]; [@b32-gmb-35-2-365]
  Xikrin                X       X                             [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]
  Yagua                 X       X                             [@b66-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Yámana                X                                     [@b38-gmb-35-2-365][^1^](#tfn28-gmb-35-2-365){ref-type="table-fn"}
  Yanomámi              X       X        X                    [@b29-gmb-35-2-365]; [@b81-gmb-35-2-365]; [@b64-gmb-35-2-365]; [@b56-gmb-35-2-365]; Silva Jr *et al.* ([@b88-gmb-35-2-365], [@b89-gmb-35-2-365])[^2^](#tfn29-gmb-35-2-365){ref-type="table-fn"}; [@b105-gmb-35-2-365]; [@b27-gmb-35-2-365]; [@b32-gmb-35-2-365]
  Yungay                X                                     [@b55-gmb-35-2-365]
  Yuracare              X                                     [@b8-gmb-35-2-365]
  Zenu                  X       X                             [@b92-gmb-35-2-365]
  Zoró                  X                X                    [@b102-gmb-35-2-365]; [@b32-gmb-35-2-365]

Ancient DNA.

Sequencing included almost half of the genome (sites 7,148--15,976).

###### 

Mitochondrial DNA haplogroup and linguistic and geographical information for the samples considered.

  Population (n)[^1^](#tfn30-gmb-35-2-365){ref-type="table-fn"}                                                  Haplogroups (%)   Language   Geographical coordinates   References                                                                     
  -------------------------------------------------------------------------------------------------------------- ----------------- ---------- -------------------------- ------------ ---- ------------------- ---------------------------------------- -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  Wayuu (89)                                                                                                     26                28         45                         0            1    Arawakan            11° N; 73° W                             [@b65-gmb-35-2-365]; [@b50-gmb-35-2-365]; [@b59-gmb-35-2-365]
  Kogi (153)                                                                                                     67                0          33                         0            0    Chibchan            11° N; 74° W                             [@b50-gmb-35-2-365]; [@b59-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Arsario (Wiwa) (76)                                                                                            63                0          37                         0            0    Chibchan            10° 25′ N; 73° 05′ W                     [@b50-gmb-35-2-365]; [@b59-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Chimila (35)                                                                                                   88                0          3                          6            3    Chibchan            10° 16′ N; 74° 4′ W                      [@b50-gmb-35-2-365]
  Arhuaco (Ijka) (134)                                                                                           87                1          12                         0            0    Chibchan            9° 04′ N; 73° 59′ W                      [@b50-gmb-35-2-365]; [@b59-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Yukpa (88)                                                                                                     0                 100        0                          0            0    Carib               8° 40′ N; 72° 41′ W                      [@b50-gmb-35-2-365]
  Zenu (107)                                                                                                     19                38         36                         5            2    Spanish             8° 30′ N; 76° W                          [@b65-gmb-35-2-365]; [@b50-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Embera (43)                                                                                                    53                35         2                          5            5    Choco               7° N; 76° 30′ W                          [@b65-gmb-35-2-365]; [@b50-gmb-35-2-365]
  Tule-Cuna (30)                                                                                                 50                27         20                         0            3    Chibchan            6° 56′ N; 76° 45′ W                      [@b50-gmb-35-2-365]
  Guane-Butaregua (33)                                                                                           12                64         0                          24           0    Chibchan            6° 15′ N; 73° 15′ W                      [@b50-gmb-35-2-365]
  Cubeo (22)                                                                                                     27                18         50                         5            0    Tucanoan            5° 9′ N; 70° 18W                         [@b92-gmb-35-2-365]
  Makiritare (10)                                                                                                20                0          70                         10           0    Carib               5° 33′ N; 65° 33′ W                      [@b94-gmb-35-2-365]
  Kali' na (Galibi) (29)                                                                                         7                 41         38                         7            7    Carib               5° 31′ N; 53° 47′ W                      [@b58-gmb-35-2-365]
  Guahibo (99)                                                                                                   52                3          33                         0            12   Guahiban            5° N; 69° W                              [@b50-gmb-35-2-365]; [@b101-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Waunana (161)                                                                                                  21                49         16                         14           0    Choco               4° 50′ N; 77° W                          [@b50-gmb-35-2-365]; [@b90-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Palikúr (64)                                                                                                   1                 47         4                          47           1    Arawakan            4° N; 51° 45′ W                          [@b56-gmb-35-2-365]; [@b58-gmb-35-2-365]
  Macushi (10)                                                                                                   10                20         30                         40           0    Carib               4° N; 60° 50′ W                          [@b94-gmb-35-2-365]
  Páez (51)                                                                                                      59                12         27                         2            0    Páez                3° 9′ N; 75° 28′ W                       [@b50-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Ocaina (2)                                                                                                     0                 0          100                        0            0    Witotoan            3° 58′ N; 68° 2′ W                       [@b92-gmb-35-2-365]
  Jebero (1)                                                                                                     0                 0          100                        0            0    Cahuapanan          3° 58′ N; 68° 2′ W                       [@b92-gmb-35-2-365]
  Piaroa (28)                                                                                                    36                11         21                         32           0    Salivan             3° 57′ N; 66° 22′ W                      [@b94-gmb-35-2-365]; [@b50-gmb-35-2-365]
  Desano (2)                                                                                                     50                0          0                          50           0    Tucanoan            3° 24′ N; 69° 40′ W                      [@b92-gmb-35-2-365]
  Wapishana (12)                                                                                                 0                 25         8                          67           0    Arawakan            3° 07′ N; 60° 03′ W                      [@b94-gmb-35-2-365]
  Emerillon (30)                                                                                                 30                70         0                          0            0    Tupi                3° N; 53° W                              [@b58-gmb-35-2-365]
  Guambiano (23)                                                                                                 4                 4          79                         13           0    Barbacoan           2° 6′ N; 76° 23′ W                       [@b50-gmb-35-2-365]
  Yanomámi (491)                                                                                                 2                 25         50                         19           4    Yanomam             2° 50′ N; 54° W                          [@b93-gmb-35-2-365], [@b94-gmb-35-2-365]); [@b29-gmb-35-2-365]; [@b64-gmb-35-2-365]; [@b105-gmb-35-2-365]; [@b89-gmb-35-2-365]
  Guayabero (30)                                                                                                 50                17         13                         0            20   Guahiban            2° 25′ N; 71° 4′ W                       [@b50-gmb-35-2-365]
  Curripaco (22)                                                                                                 41                36         23                         0            0    Arawakan            2° 10′ N; 68° 54′ W                      [@b50-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Tiriyó (32)                                                                                                    9                 19         22                         47           3    Carib               2° N; 56° W                              [@b56-gmb-35-2-365]; [@b89-gmb-35-2-365]
  Nukak (20)                                                                                                     0                 20         80                         0            0    Maku                1° 44′ N; 70° 44′ W                      [@b50-gmb-35-2-365]
  Apalaí (120)                                                                                                   37                1          30                         32           0    Carib               1° 20′ N; 54° 40′ W                      [@b56-gmb-35-2-365]; [@b58-gmb-35-2-365]
  Cayapa (120)                                                                                                   29                40         9                          22           0    Barbacoan           1° 17′ N; 78° 50′ W                      [@b74-gmb-35-2-365]
  Wayampi (99)                                                                                                   62                11         8                          19           0    Tupi                1° N; 53° W                              [@b81-gmb-35-2-365]; [@b56-gmb-35-2-365]; [@b89-gmb-35-2-365]; [@b58-gmb-35-2-365]
  Siona (12)                                                                                                     75                17         8                          0            0    Tucanoan            0° 6′ N; 75° 36′ W                       [@b50-gmb-35-2-365]
  Pasto (9)                                                                                                      67                33         0                          0            0    Barbacoan           0° 58′ N; 77° 44′ W                      [@b50-gmb-35-2-365]
  Yagua (12)                                                                                                     25                0          67                         8            0    Peba-Yaguan         0° 51′ N; 72° 27′ W                      [@b92-gmb-35-2-365]
  Ingano (111)                                                                                                   18                38         42                         0            2    Quechuan            0° 50′ N; 77° W                          [@b65-gmb-35-2-365]; [@b50-gmb-35-2-365]; [@b92-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Tucano (17)                                                                                                    0                 18         47                         35           0    Tucanoan            0° 42′ N; 69° 53′ W                      [@b50-gmb-35-2-365]
  Coreguaje (69)                                                                                                 4                 20         66                         6            4    Tucanoan            0° 38′ N; 76° 8′ W                       [@b50-gmb-35-2-365]; [@b90-gmb-35-2-365]
  Awa-Juriti (18)                                                                                                0                 72         11                         0            17   Tucanoan            0° 16′ N; 70° 45′ W                      [@b56-gmb-35-2-365]
  Muinane (19)                                                                                                   11                21         37                         26           5    Witotoan            0° 11′ N; 73° 25′ W                      [@b50-gmb-35-2-365]
  Poturujara (23)                                                                                                44                0          26                         30           0    Tupi                0° 18′ S; 55° 18′ W                      [@b56-gmb-35-2-365]; [@b89-gmb-35-2-365]
  Katuena (23)                                                                                                   26                9          35                         30           0    Carib               0° 40′ S; 57° 30′ W                      [@b56-gmb-35-2-365]; [@b89-gmb-35-2-365]
  Wai-wai (26)                                                                                                   15                15         43                         27           0    Carib               0° 40′ S; 58° W                          [@b13-gmb-35-2-365]
  Urubu Kaapor (42)                                                                                              21                31         14                         29           5    Tupi                2°--3° S; 46°--47° W                     Torroni *et al.* ([@b93-gmb-35-2-365], [@b94-gmb-35-2-365]); [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]
  Huitoto (35)                                                                                                   23                3          25                         46           3    Witotoan            2° 14′ S; 72° 19′ W                      [@b50-gmb-35-2-365]; [@b92-gmb-35-2-365]
  Arara (70)                                                                                                     54                20         26                         0            0    Carib               3° 30′--4° 20′ S; 53° 0′--54° 10′ W      [@b56-gmb-35-2-365]; [@b73-gmb-35-2-365]; [@b89-gmb-35-2-365]; Bisso-Machado (2010, MSc Dissertation, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.)
  Awa-Guajá (53)                                                                                                 13                87         0                          0            0    Tupi                3° 30′ S; 46° 40′ W                      [@b56-gmb-35-2-365]
  Asurini (24)                                                                                                   4                 54         17                         21           4    Tupi                3° 35′--4° 12′ S; 49° 40′--52° 26′ W     [@b56-gmb-35-2-365]
  Piapoco (39)                                                                                                   18                3          15                         5            59   Arawakan            3° 36′ S; 70° 23′ W                      [@b92-gmb-35-2-365]
  Puinave (19)                                                                                                   5                 16         58                         16           5    Puinave             3° 36′ S; 70° 23′ W                      [@b92-gmb-35-2-365]
  Sáliba (13)                                                                                                    15                0          55                         15           15   Salivan             3° 49′ S; 70° 9′ W                       [@b92-gmb-35-2-365]
  Ticuna (371)                                                                                                   20                11         35                         33           1    Ticuna              4° S; 69° 58′ W                          [@b84-gmb-35-2-365]; [@b65-gmb-35-2-365]; [@b92-gmb-35-2-365]; [@b60-gmb-35-2-365]; [@b76-gmb-35-2-365]
  Parakanã (31)                                                                                                  6                 39         32                         23           0    Tupi                5° 22′ S; 51° 17′ W                      [@b56-gmb-35-2-365]; Bisso-Machado (2010, MSc Dissertation)
  Xikrin (33)                                                                                                    30                64         3                          3            0    Macro-Ge            5° 55′ S; 51° W                          [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]; Bisso-Machado (2010, MSc Dissertation)
  Suruí (44)                                                                                                     7                 4          0                          89           0    Tupi                5° 58′ -10° 50′ S; 48° 39′ -61° 10′ W    [@b13-gmb-35-2-365]; [@b56-gmb-35-2-365]
  Araweté (18)                                                                                                   39                0          50                         11           0    Tupi                5° 9′ S; 52° 22′ W                       [@b56-gmb-35-2-365]
  Munduruku (92)                                                                                                 12                17         9                          58           4    Tupi                6° 23′ S; 59° 9′ W                       Torroni *et al.* ([@b93-gmb-35-2-365], [@b94-gmb-35-2-365]); [@b56-gmb-35-2-365]; [@b57-gmb-35-2-365]; Bisso-Machado (2010, MSc Dissertation)
  Marubo (10)                                                                                                    10                0          60                         30           0    Panoan              6° 47′ S; 72° 80′ W                      [@b94-gmb-35-2-365]
  Jamamadi (23)                                                                                                  0                 0          96                         4            0    Arauan              7° 15′ S; 66° 41′ W                      [@b56-gmb-35-2-365]; Bisso-Machado (2010, MSc Dissertation)
  Yungay (38)                                                                                                    5                 45         34                         16           0    Quechuan            7° 26′ S; 77° 4′ W                       [@b55-gmb-35-2-365]
  Ancash (33)                                                                                                    9                 52         18                         21           0    Quechua             7° 41′ S; 77° 6′ W                       [@b54-gmb-35-2-365]
  Gorotire (11)                                                                                                  28                18         18                         36           0    Macro-Ge            7° 44′ S; 51° 10′ W                      Bisso-Machado (2010, MSc Dissertation)
  Krahó (14)                                                                                                     29                57         14                         0            0    Macro-Ge            8° S; 47° 15′ W                          [@b94-gmb-35-2-365]
  Kuben-Kran-Kegn (19)                                                                                           58                26         6                          10           0    Macro-Ge            8° 10′ S; 52° 8′ W                       Bisso-Machado (2010, MSc Dissertation)
  Mekranoti (19)                                                                                                 26                63         11                         0            0    Macro-Ge            8° 40′ S; 54° W                          [@b27-gmb-35-2-365]; Bisso-Machado (2010, MSc Dissertation)
  Kubenkokre (4)                                                                                                 0                 100        0                          0            0    Macro-Ge            8° 43′ S; 53° 23′ W                      [@b57-gmb-35-2-365]
  Kayapó (13)                                                                                                    46                54         0                          0            0    Macro-Ge            9° S; 53° W                              [@b56-gmb-35-2-365]
  Karitiana (19)                                                                                                 0                 11         0                          89           0    Tupi                9° 30′ S; 64° 15′ W                      [@b56-gmb-35-2-365]
  Cinta-Larga (45)                                                                                               25                0          20                         53           2    Tupi                9° 50′--12° 30′ S; 59° 10′--60° 50′ W    [@b56-gmb-35-2-365]; [@b27-gmb-35-2-365]; Bisso-Machado (2010, MSc Dissertation)
  Gavião (27)                                                                                                    15                15         0                          70           0    Tupi                10° 10′ S; 61° 8′ W                      [@b102-gmb-35-2-365]
  Tupe (16)                                                                                                      0                 69         31                         0            0    Aymaran             10° 16′ S; 75° 47′ W                     [@b55-gmb-35-2-365]
  Txukahamãe (2)                                                                                                 100               0          0                          0            0    Macro-Ge            10° 20′ S; 53° 5′ W                      [@b27-gmb-35-2-365]
  Zoró (30)                                                                                                      20                7          13                         60           0    Tupi                10° 20′ S; 60° 20′ W                     [@b102-gmb-35-2-365]
  Matsiguenga (38)                                                                                               5                 92         0                          3            0    Arawakan            10° 47′--12° 51′ S; 73° 17′ -70° 44′ W   [@b58-gmb-35-2-365]
  Kokraimoro (2)                                                                                                 50                50         0                          0            0    Macro-Ge            10° 49′ S; 55° 27′ W                     [@b57-gmb-35-2-365]
  Pacaás Novos (Wari) (30)                                                                                       40                30         27                         3            0    Chapacura-Wanh am   11° 8′ S; 65° W                          Bisso-Machado (2010, MSc Dissertation)
  Tayacaja (61)                                                                                                  21                33         13                         30           3    Quechuan            12° 24′ S; 74° 34′ W                     [@b35-gmb-35-2-365]
  Arequipa (22)                                                                                                  9                 68         14                         9            0    Quechua             13° 13′ S; 72° 11′ W                     [@b35-gmb-35-2-365]
  Trinitario (35)                                                                                                14                40         37                         3            6    Arawakan            14° S; 65° W                             [@b7-gmb-35-2-365]
  Xavánte (25)                                                                                                   16                84         0                          0            0    Macro-Ge            14° S; 52° 30′ W                         [@b102-gmb-35-2-365]
  Movima (22)                                                                                                    9                 9          64                         18           0    Movima              14° 26′ S; 65° 53′ W                     [@b7-gmb-35-2-365]
  Quechua (232)                                                                                                  14                62         15                         9            0    Quechuan            14° 30′ S; 69° W                         [@b63-gmb-35-2-365]; [@b7-gmb-35-2-365]; [@b89-gmb-35-2-365]; [@b55-gmb-35-2-365]; [@b21-gmb-35-2-365]; [@b6-gmb-35-2-365]; [@b39-gmb-35-2-365]
  Chimane (Moseten) (71)                                                                                         39                54         3                          0            4    Chimane             14° 41′ S; 66° 50′ W                     [@b7-gmb-35-2-365]; [@b21-gmb-35-2-365];
  Ignaciano (22)                                                                                                 18                36         41                         0            5    Arawakan            15° 1′ S; 66° 4′ W                       [@b7-gmb-35-2-365]
  Uro (64)                                                                                                       11                69         9                          11           0    Uru-Chipaya         15° 45′ S; 69° 53′ W                     [@b6-gmb-35-2-365]
  Yuracare (28)                                                                                                  39                32         21                         4            4    Yuracare            17° S; 65° W                             [@b7-gmb-35-2-365]
  Aymara (411)                                                                                                   4                 76         8                          11           1    Aymaran             17° 68′ S; 69° 16′ W                     [@b63-gmb-35-2-365]; [@b29-gmb-35-2-365]; [@b7-gmb-35-2-365]; [@b55-gmb-35-2-365]; [@b21-gmb-35-2-365]; [@b6-gmb-35-2-365]; [@b39-gmb-35-2-365]
  Ayoreo (91)                                                                                                    0                 0          83                         17           0    Zamucoan            19° S; 60° 30′ W                         [@b26-gmb-35-2-365]
  Wichí (199)                                                                                                    12                51         7                          29           1    Mataco-Guaicuru     22° 28′ S; 62° 70′ W                     [@b94-gmb-35-2-365]; [@b9-gmb-35-2-365]; [@b17-gmb-35-2-365]; [@b24-gmb-35-2-365]; [@b18-gmb-35-2-365]
  Chorote (34)                                                                                                   15                44         23                         18           0    Mataco-Guaicuru     22° 90′ S; 65° 40′ W                     [@b9-gmb-35-2-365]; [@b17-gmb-35-2-365]
  Humahuaca (46)                                                                                                 11                68         17                         4            0    Spanish             23° 11′ S; 65° 20′ W                     [@b25-gmb-35-2-365]
  Aché (63)                                                                                                      10                90         0                          0            0    Tupi                23° 30′--24° 10′ S; 55° 50′--56° 30′ W   [@b82-gmb-35-2-365]
  Atacameño (79)                                                                                                 13                73         10                         4            0    Atacama             23° 50′ S; 68° W                         [@b4-gmb-35-2-365]; [@b63-gmb-35-2-365]; [@b61-gmb-35-2-365]
  Guarani (249)                                                                                                  77                6          9                          6            2    Tupi                23° 6′ S; 55° 12′ W                      [@b89-gmb-35-2-365]; [@b57-gmb-35-2-365]; [@b36-gmb-35-2-365]
  Pilagá (41)                                                                                                    5                 37         27                         29           2    Mataco-Guaicuru     24° S; 59° W                             [@b24-gmb-35-2-365]; [@b18-gmb-35-2-365]
  Coya (60)                                                                                                      13                57         23                         5            2    Coya                25° 30′ S; 67° 28′ W                     [@b2-gmb-35-2-365]
  Toba (80)                                                                                                      15                43         5                          37           0    Mataco-Guaicuru     26° S; 58° W                             [@b9-gmb-35-2-365]; [@b24-gmb-35-2-365]; [@b42-gmb-35-2-365]; [@b18-gmb-35-2-365]
  Jujuy (19)                                                                                                     16                58         16                         10           0    Spanish             27° 27′ S; 58° 59′ W                     [@b25-gmb-35-2-365]
  Kaingang (79)                                                                                                  47                4          48                         0            1    Macro-Ge            28° S; 51° 20′ W                         [@b27-gmb-35-2-365]; [@b57-gmb-35-2-365]
  Mocoví (5)                                                                                                     80                0          0                          20           0    Mataco-Guaicuru     29° 51′ S; 59° 56′ W                     [@b90-gmb-35-2-365]
  Pehuenche (205)                                                                                                2                 9          40                         49           0    Araucanian          37° 43′ S; 71° 16′ W                     [@b63-gmb-35-2-365]; [@b67-gmb-35-2-365], [@b68-gmb-35-2-365])
  Mapuche (314)                                                                                                  5                 23         32                         36           4    Araucanian          39° 10′--41° 20′ S; 68° 37′--70° 22′ W   [@b41-gmb-35-2-365]; [@b43-gmb-35-2-365]; [@b4-gmb-35-2-365]; [@b9-gmb-35-2-365]; [@b68-gmb-35-2-365]
  Huilliche (207)                                                                                                4                 28         20                         48           0    Araucanian          41° 16′ S; 73° W                         [@b4-gmb-35-2-365]; [@b63-gmb-35-2-365]; [@b61-gmb-35-2-365]
  Aónikenk^[3](#tfn32-gmb-35-2-365){ref-type="table-fn"},\ [4](#tfn33-gmb-35-2-365){ref-type="table-fn"}^ (15)   0                 0          27                         73           0    Chon                45° S; 71° W                             Lalueza (1995, PhD thesis, Universitat de Barcelona, Barcelona, Spain)
  Tehuelche[^4^](#tfn33-gmb-35-2-365){ref-type="table-fn"} (29)                                                  0                 20         24                         56           0    Chon                45° S; 71° W                             [@b68-gmb-35-2-365]
  Yámana[^3^](#tfn32-gmb-35-2-365){ref-type="table-fn"} (Yaghan) (32)                                            0                 0          63                         37           0    Yámana              47° S; 74° W                             Lalueza (1995, PhD thesis); Moraga *et al.* ([@b67-gmb-35-2-365], [@b68-gmb-35-2-365])
  Kawéskar[^2^](#tfn31-gmb-35-2-365){ref-type="table-fn"} (Alacaluf) (19)                                        0                 0          16                         84           0    Alacalufan          49° S; 74° W                             Lalueza (1995, PhD thesis)
  Selknam[^2^](#tfn31-gmb-35-2-365){ref-type="table-fn"} (Ona) (16)                                              0                 0          56                         38           6    Chon                54° S; 74° W                             Lalueza (1995, PhD thesis); [@b38-gmb-35-2-365]

Arranged according to latitude.

Probably of non-Amerindian origin.

Ancient DNA.

Aónikenk and Tehuelche are the same tribe separated by time. Aónikenk refers to ancient DNA.

###### 

Mitochondrial DNA haplogroup frequencies by geography[^1^](#tfn34-gmb-35-2-365){ref-type="table-fn"}.

  Geographic divisions     No. of populations   No. of individuals   Haplogroups (%)                  
  ------------------------ -------------------- -------------------- ----------------- ---- ---- ---- ---
  Amazonia                 55                   2410                 20                21   31   25   3
  Central Plateau          2                    39                   21                74   5    0    0
  Southern Brazil          2                    328                  70                6    18   4    2
  Chaco                    6                    479                  10                43   22   24   1
  Southern South America   3                    726                  4                 20   31   43   2
  Tierra del Fuego         5                    111                  0                 5    39   55   1
  Andes                    35                   2604                 27                45   20   7    1
  Total                    108                  6697                                                  

AMOVA results: (a) Among geographic divisions: 6.2%; (b) Among populations within geographic divisions: 19.5%; (c) Within populations: 74.3%. The three values are statistically significant.

###### 

Mitochondrial DNA haplogroup frequencies by language[^1^](#tfn35-gmb-35-2-365){ref-type="table-fn"}.

  Language          No. of populations   No. of individuals   Haplogroups (%)                  
  ----------------- -------------------- -------------------- ----------------- ---- ---- ---- ----
  Tupi              16                   889                  38                24   10   27   1
  Macro-Ge          11                   221                  37                38   21   3    1
  Carib             9                    408                  24                32   25   18   1
  Chibchan          6                    461                  69                6    22   2    1
  Mataco-Guaicuru   5                    359                  13                46   11   29   1
  Arawakan          8                    321                  16                38   24   13   9
  Araucanian        3                    726                  4                 20   31   43   2
  Choco             2                    204                  28                46   13   12   1
  Chon              3                    60                   0                 10   33   55   2
  Tucanoan          6                    140                  14                26   48   8    4
  Aymaran           2                    427                  4                 76   9    10   1
  Barbacoan         3                    152                  28                34   19   19   0
  Guahiban          2                    129                  51                6    29   0    14
  Witotoan          3                    56                   18                9    32   37   4
  Salivan           2                    41                   29                7    32   27   5
  Quechuan          6                    497                  14                51   23   11   1
  Other             21                   1606                 13                26   40   19   2
  Total             108                  6697                                                  

AMOVA results: (a) Among language groups: 6.6%; (b) Among populations within language groups: 20.1%; (c) Within populations: 73.3%. The three values are statistically significant.
