Examples of indigenous Amerindian mtDNA haplogroups (inherited in the maternal line) include A2, A2d, A2f1a, A2w1, A4, B2, B2a5, C1b6, C1b14, C1c, D2a, D4h3a, X2a1b, X2g, and many others. For example, A2 is common in Mexico, C1b2 and C1b4 are found in Puerto Rico, C4c1a is found among the Cherokee, and X2a1 and X2g are found among the Ojibwe.
Indigenous Amerindian Y-DNA haplogroups (inherited in the paternal line) are within branches of Q, R1, and C. They include Q-M3, Q-M19, Q-L54, Q-Z780, Q-MEH2, Q-SA01, Q-M346, Q-P89.1, Q-NWT01, R1-M173, and C-P39. 83 percent of indigenous South American males belong to Q-M3. Q-M19 is especially common among the Ticunas of the Amazon. C-P39's prevalence peaks among the Athabaskans. Note that R1 is the genetic ancestor of R1a and R1b, but those two branches aren't native to Amerindians.
Much of the Amerindians' genetic diversity was lost due to a massive decrease in the Amerindian population during the early colonialist era. The causes included Europeans diseases for which the natives had no immunity (including smallpox and measles) and, in some cases, wars. As a result, some mtDNA haplogroups that used to exist up to the 1500s have become extinct. Many branches of A2, B2, C1, and D1 were lost, and there once were Amerindians bearing branches of M.
Family Tree DNA, based in Houston, Texas, U.S.A., is a direct-to-consumer company that performs testing of mtDNA and Y-DNA lines. This can verify your Amerindian ancestry in a particular uniparental lineage. If you belong to a bonafide Amerindian lineage, you can apply to join such projects hosted by the company as "American Indian Proj", "Q1a3a1-AmerIndian", "Worldwide Mitochondrial Haplogroup B Project", and/or "A2 mtDNA Haplogroup Project".
"Mayans: a Y chromosome perspective" by David Perez-Benedico, Joel La Salvia, et al. in European Journal of Human Genetics 24 (August 2016): 1352-1358. ("overall, the Mayan populations as a group are highly homogeneous, basically made up of only two autochthonous [Y-DNA] haplogroups, Q1a2a1a1*-M3 and Q1a2a1*-L54.")
"Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas" by Bastien Llamas, Lars Fehren-Schmitz, et al. in Science Advances 2:4 (April 1, 2016): e1501385. ("We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, [...] All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. [...] The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.")
"The Genetic History of Peruvian Quechua-Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations" by José Raul Sandoval Sandoval, D. R. Lacerda, et al. in Annals of Human Genetics 80:2 (March 2016): pages 88-101.
"Admixture and Genetic Diversity Distribution Patterns of Non-Recombining Lineages of Native American Ancestry in Colombian Populations" by Catarina Xavier, Juan José Builes, et al. in PLoS ONE 10:3 (March 16, 2015): e0120155.
"Mitochondrial variation among the Aymara and the signatures of population expansion in the central Andes" by Ken Batai and Sloan R. Williams in American Journal of Human Biology 26:3 (May-June 2014): pages 321-330.
"Mitochondrial DNA variability among six South American Amerindian villages from the Pano linguistic group" by Celso T. Mendes-Junior and Aguinaldo L. Simões in Human Biology 86:2 (Spring 2014): pages 93-104.
"Genetic uniqueness of the Waorani tribe from the Ecuadorian Amazon" by S. Cardoso, M. A. Alfonso-Sánchez, et al. in Heredity 108:6 (June 2012): pages 609–615. 94% of Waorani have the mtDNA haplogroup A2.
"Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations" by M. C. Dulik, A. C. Owings, et al. in Proceedings of the National Academy of Sciences of the United States of America 109:22 (May 29, 2012): pages 8471-8476.
"Beringian Standstill and Spread of Native American Founders" by Erika Tamm, Toomas Kivisild, et al. in PLoS ONE 2:9 (September 5, 2007): e829.
"Mitochondrial DNA diversity of the Amerindian populations living in the Andean Piedmont of Bolivia: Chimane, Moseten, Aymara and Quechua" by A. Corella, F. Bert, et al. in Annals of Human Biology 34:1 (January-February 2007): pages 34-55.
"Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence" by T. G. Schurr and S. T. Sherry in American Journal of Human Biology 16:4 (July-August 2004): pages 420-439.
"Mitochondrial DNA diversity in the Llanos de Moxos: Moxo, Movima and Yuracare Amerindian populations from Bolivia lowlands" by F. Bert, A. Corella, et al. in Annals of Human Biology 31:3 (January-February 2004): pages 9-28.
"The dual origin and Siberian affinities of Native American Y chromosomes" by J. T. Lell, R. I. Sukernik, et al. in American Journal of Human Genetics 70:1 (January 2002): pages 192-206.
"mtDNA Variation among Greenland Eskimos: The Edge of the Beringian Expansion" by Juliette Saillard, Peter Forster, et al. in American Journal of Human Genetics 67:3 (September 2000)): pages 718-726.
Autosomal DNA represents the vast majority of your DNA and is comprised of sections of DNA you inherited from all of your great-great-grandparents and many of their ancestors.
Amerindian ancestry represents a blend between ancient East Asian ancestry (their majority element, approximately 70 percent) and ancient North Asian ancestry that is also related to West Eurasians.
Among the major direct-to-consumer autosomal DNA testing companies, AncestryDNA is currently the best at detecting and reporting accurate quantities of Amerindian ancestry. This is due in part to the reference samples they compare their customers to. However, as good as it can be, AncestryDNA occasionally somewhat overestimates the amount of Amerindian ancestry for some of its testers, and occasionally they assign some "Amerindian" ancestry to some peoples of northern Eurasia including some Russians and Mongolians.
MyOrigins version 2.0, introduced on April 4, 2017 as part of Family Tree DNA's Family Finder autosomal DNA test, divides Amerindian DNA into two categories: "North and Central America" and "South America". Some people occasionally get false trace readings of less than 2% of one of these elements, but if you score more than a trace it usually represents real Amerindian ancestry from the Americas as opposed to shared ancient origins in Siberia.
Out of the free ethnicity estimation calculators at GEDmatch, Eurogenes K36 is among the best at minimizing noise or false readings of Amerindian ancestry, although it doesn't always do a perfect job. Eurogenes K36's reference population consists of 4 Colombians, 6 Karitiana, 4 Mayans, 5 Peruvians, 7 Pima, and 3 Surui.
Indigenous reference populations used by GEDmatch's free MDLP K13 Ultimate calculator include Miwok, Tsimsian, Athabaskan, Haida, Quechua, Chachi, Chilote, Totonac, Zapotec, Pima, Mixtec, and Wayuu, among others. However, this calculator gives noise readings for Amerindian affinity to some people who don't really have any Amerindian ancestry.
GEDmatch's free MDLP K23b calculator's Amerindian estimates are based on 100 Ticuna samples, while its Arctic element is based on 94 Eskimo samples. This calculator also gives out noise readings.
Individual members of the Navajo and Yaqui tribes from the United States, the Nahua tribe from Mexico, and Mayan peoples from Guatemala are among those who have submitted their DNA to 23andMe for autosomal testing.
The ALlele FREquency Database compiled by Kenneth K. Kidd of Yale University includes data on particular autosomal alleles found in the Cheyenne, Muscogee (Creek), Pima, Maya peoples of North America and the Guihiba, Karitiana, Quechua, Surui, and Ticuna peoples of South America. For instance, the 1540C allele (of East Asian origin) in the EDAR gene is reported by the database to be found among 95.5% of Cheyenne, 59% of Muscogee, 99% of Pima from Arizona, 97.7% of Pima from Mexico (129 out of 132 individuals in two studies), 86.6% of Maya people from Mexico's Yucatán Peninsula (123 out of 142 individuals in two studies), 77.3% of Guihiba from Colombia, 90.5% of Quechua, 94.5% of Ticuna, 77.5% of Surui (79 out of 102 individuals in two studies), and 99.3% of Karitiana (137 out of 138 individuals in two studies).
"Genomic evidence for the Pleistocene and recent population history of Native Americans" by Maanasa Raghavan, Matthias Steinrücken, et al. in Science (July 21, 2015). ("Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians.")
"Reconstructing Native American Population History" by David Reich, Nick Patterson, et al. in Nature 488:7411 (August 16, 2012): pages 370-374. ("We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream.")
"A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity" by Keith Hunley, Kiela Gwin, et al. in PLoS ONE 11:8 (August 31, 2016): e0161018. Includes autosomal DNA data from such tribes as Ojibwa and Cree in Canada, and in Latin America the following: Pima, Maya, Zapotec, Mixtec, Guaymi, Cabecar, Quechua, Inga, Wayuu, Piapoco, Guarani, Karitiana, Ache, and more tribes. Examines their degrees of Amerindian DNA versus foreign admixture, and differences in regional clusters of Amerindian DNA within the Americas. ("We found that 1) European and East Asian ancestry estimates decline as K [number of ancestral clusters] increases, especially in Native Canadian populations, 2) a north-south decline in gene diversity is driven by low diversity in Amazonian and Paraguayan populations, not serial founder effects from Beringia, 3) controlling for non-Native American ancestry, populations in the Andes and Mesoamerica have higher gene diversity than populations in other regions, and 4) patterns of genetic and linguistic diversity are poorly correlated.")
"Admixture and Genetic Diversity Distribution Patterns of Non-Recombining Lineages of Native American Ancestry in Colombian Populations" by Catarina Xavier, Juan José Builes, et al. in PLoS ONE 10:3 (March 16, 2015): e0120155.
"Ancestry informative markers in Amerindians from Brazilian Amazon" by M. R. Luizon, Celso T. Mendes-Junior, et al. in American Journal of Human Biology 20:1 (January-February 2008): pages 86-90.
"Rare variants and autosomal haplotypes reveal the Siberian roots of North American Na-Dene populations" by Pavel Flegontov, N. Ezgi Altınışıkı, et al. in the Abstract Book for the 6th International Conference of the Series "DNA Polymorphisms in Human Population", 7-10 December 2016 on page 18. ("All methods detected Central and West Siberian ancestry exclusively in a fraction of Na-Dene individuals, but not in other Native Americans. [...] we have modelled a gene flow from a Siberian population that split 6,500-7,000 years ago into the ancestors of Na-Dene. Our results are consistent with a Paleo-Eskimo admixture into the First American ancestors of Na-Dene, and a much later and less extensive bidirectional admixture was detected between Na-Dene and Neo-Eskimos.")
The HLA is located on chromosome 6 and regulates a person's immune system. Many different HLA types exist in world populations and some are more frequent in particular continents and regions.
"A time transect of exomes from a Native American population before and after European contact" by John Lindo, Emilia Huerta-Sánchez, et al. in Nature Communications 7 (November 15, 2016): article number 13175. A discussion focusing on HLA types among pre-modern and modern First Nations peoples of British Columbia including Tsimshian people, who have become admixed with Europeans ("we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. [...] The important immune function of HLA-DQA1 supports an ancient adaptation to the environments of the Americas. The modern individuals show a marked decrease in the frequency of the associated alleles [...] This decrease is likely due to the environmental change associated with European colonization [...] the selection pressure shift could correlate to the European-borne epidemics of the 1800s")
"Origin of Mayans according to HLA genes and the uniqueness of Amerindians" by E. Gómez-Casado, J. Martínez-Laso, et al. in Tissue Antigens 61:6 (June 2003): pages 425-436.
Many speakers of the Spanish, Portuguese, French, and English languages in the Americas descend in part from Amerindians. These include the peoples of Acadia in northeastern Canada, of Mexico, of Puerto Rico, of Brazil, and many other places. In Virginia, Pocahontas of the Powhatan tribe married an Englishman and they have thousands of descendants alive today in the United States.
A small proportion of Amerindian ancestry is also found among Spaniards living in Spain. Some of them descend from the Aztec Empire ruler Moctezuma II.
Small percentages of Amerindian ancestry are found among some Filipinos of the Philippines and Chamorros of Guam due to immigration of part-Amerindian Mexicans centuries ago.
"The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States" by Katarzyna Bryc, Eric Y. Durand, et al. in American Journal of Human Genetics 96:1 (January 8, 2015): pages 37-53. Table 1 shows that African-Americans on average have 0.8% genome-wide Native American ancestry. The authors estimate that "about 22% of African Americans carry some Native American ancestry". European-Americans on average have 0.18% genome-wide Native American ancestry. Only a small percentage of European-Americans have any at all, and the authors estimate that Native American admixture is most common among European-Americans who live in Louisiana, North Dakota, and various other southwestern and western U.S. states. It's no surprise that Latinos in the U.S. have far higher proportions of Native American ancestry.
"Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data" by Simon Gravel, Fouad Zakharia, et al. in PLoS Genetics 9:12 (December 26, 2013): e1004023.
"Tracing the genomic ancestry of Peruvians reveals a major legacy of pre-Columbian ancestors" by José Raul Sandoval Sandoval, Alberto Alcibíades Salazar Granara, et al. in Journal of Human Genetics 58:9 (September 2013): pages 627-634. ("our analysis indicated that populations from all 25 Peruvian locations had predominantly Amerindian genetic ancestry.") Table 1 reveals that the Native American ancestral proportion among their sample of 551 Peruvians is 83%.
"Native American Admixture in the Quebec Founder Population" by Claudia Moreau, Jean-François Lefebvre, et al. in PLoS ONE 8:6 (June 12, 2013): e65507.
"Fast and accurate inference of local ancestry in Latino populations" by Yael Baran, Bogdan Pasaniuc, et al. in Bioinformatics 28:10 (May 15, 2012): pages 1359-1367.
"The Genetic Legacy of the Pre-Colonial Period in Contemporary Bolivians" by Patricia Taboada-Echalar, Vanesa Álvarez-Iglesias, et al. in PLoS ONE 8:3 (March 20, 2013): e58980.
"Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups" by Gabriela Martínez-Cortés, Joel Salazar-Flores, et al. in American Journal of Physical Anthropology 151:4 (August 2013): pages 526-537. ("The predominant maternal ancestry was Native American (92.9%), including Haplogroups A, B, C, and D (47, 23.7, 15.9, and 6.2%, respectively).")
"Admixture and population structure in Mexican-Mestizos based on paternal lineages" by Gabriela Martínez-Cortés, Joel Salazar-Flores, et al. in Journal of Human Genetics 57:9 (September 2012): pages 568-574. The average proportion of paternal-line Amerindian ancestry in Mexican Mestizos is 30.8%.
"Decrypting the Mitochondrial Gene Pool of Modern Panamanians" by Ugo A. Perego, Hovirag Lancioni, et al. in PLoS ONE 7:6 (June 4, 2012): e38337. 83% of the people of Panama belong to the Amerindian mtDNA haplogroups; of them, 51% belong to A2, including subclades A2ad and A2af.
"Typing of Amerindian Kichwas and Mestizos from Ecuador with the SNPforID multiplex" by L. Poulsen, C. Børsting, et al. in Forensic Science International Genetics 5:4 (August 2011): pages e105-e107.
"Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database" by M. C. Bobillo, B. Zimmermann, et al. in International Journal of Legal Medicine 124:4 (July 2010): pages 263-268. ("The Amerindian [mtDNA] haplogroups were most frequent in the north and south [of Argentina] representing more than 60% of the sequences. A slightly different situation was observed in central Argentina where the Amerindian haplogroups represented less than 50%")
"Heterogeneity in Genetic Admixture across Different Regions of Argentina" by Sergio Avena, Marc Via, et al. in PLoS ONE 7:4 (April 10, 2012): e34695. Argentinians on average have 31% Indigenous American ancestry with their typical range being between 28% to 33%.
"Sex-specific genetic admixture of Mestizos, Amerindian Kichwas, and Afro-Ecuadorans from Ecuador" by Fabrico González-Andrade, Dora Sánchez, et al. in Human Biology 79:1 (February 2007): pages 51-77. On average, Ecuadorian Mestizos have Amerindian Y chromosomal lineages at the frequency of 28%.
"Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas" by Joshua Mark Galanter, Juan Carlos Fernandez-Lopez, et al. in PLoS Genetics 8:3 (March 8, 2012): e1002554. On average, Puerto Ricans have 12% Amerindian ancestry autosomally. The study found that most Mexicans have much more Amerindian admixture than that.
"Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers" by Beatriz Marcheco-Teruel, Antonio Salas, et al. in PLoS Genetics 10:7 (July 24, 2014): e1004488. On average, Cubans have 8% Amerindian ancestry autosomally, but the proportions are higher in eastern Cuba specifically Granma (15%), Holguín (12%), and Las Tunas (12%). About 34.5% of Cubans have maternal lines tracing back to Amerindians but the proportion is again higher among those in Holguín (59%) and Las Tunas (58%). Only 0.5% of Cuban paternal lines had Amerindian ancestors.
"Reconstructing the Population Genetic History of the Caribbean" by Andrés Moreno-Estrada, Simon Gravel, et al. in PLoS Genetics 9:11 (November 14, 2013): e1003925. Based largely on samples from Cubans, Dominicans, and Puerto Ricans, they wrote "we find evidence of a high Native American [...] female contribution in Caribbean populations." Also, "Colombians and most Hondurans cluster closer to Chibchan-speaking groups from Western Colombia and Central America, including the Kogi, Embera, and Waunana. In contrast, most Caribbean islanders cluster with Amazonian groups from Eastern Colombia, Brazil, and Guiana."
"Further evidence of an Amerindian contribution to the Polynesian gene pool on Easter Island" by Erik Thorsby, S. T. Flåm, et al. in Tissue Antigens 73:6 (June 2009): pages 582-585. Although the indigenous Rapa Nui people of Easter Island, in the southeastern Pacific Ocean, have Polynesian origins and don't currently share any mtDNA or Y-DNA lineages with Amerindians, they do sometimes have HLA alleles of Amerindian origin.
"The Polynesian gene pool: an early contribution by Amerindians to Easter Island" by Erik Thorsby in Philosophical Transactions of the Royal Society B: Biological Sciences 367:1590 (2012).
"Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans" by J. Víctor Moreno-Mayar, Simon Rasmussen, et al. in Current Biology 24:21 (November 3, 2014) pages 2518-2525.
"Genetic Evidence for a Contribution of Native Americans to the Early Settlement of Rapa Nui (Easter Island)" by Erik Thorsby in Frontiers in Ecology and Evolution 4 (2016).
DNA.LAND, a non-profit research project by the New York Genome Center, accepts uploads of data from customers of AncestryDNA, Family Tree DNA, and 23andMe. DNA.LAND attempts to separate non-specific "Native American" from "Amazonian" beginning on April 8, 2016.
The reference samples for their "Native American" category are: Bolivians in Bolivia, Piapoco in Colombia, Mayans in Mexico, Mixe in Mexico, Mixtec in Mexico, Pima in Mexico, and Zapotec in Mexico.
The reference samples for their "Amazonian" category are: Karitiana in Brazil and Surui in Brazil.
Below are DNA.LAND's estimates for some old samples who didn't have post-Columbian admixture:
MARC1492: Mi'kmaq woman from Listuguj, Quebec, Canada who lived about 400 years ago, from "Statistics for Eight Holocene-Aged American Ancient DNA Samples" by Maanasa Raghavan, et al. in Science (July 21, 2015):
NA41: Pre-Columbian Peruvian from the site Laguna de los Condores in northeastern Peru, from "Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries" by Meredith L. Carpenter, et al. in The American Journal of Human Genetics 93:5 (November 7, 2013): pages 852-864:
NA40: Pre-Columbian Peruvian from the site Laguna de los Condores in northeastern Peru circa 1000-1500 C.E., part of the Chachapoya culture (same source as above):
NA42: Pre-Columbian Peruvian from the site Laguna de los Condores in northeastern Peru circa 1000-1500 C.E., part of the Chachapoya culture (same source as above):
NA39: Pre-Columbian Peruvian from the site Laguna de los Condores in northeastern Peru circa 1000-1500 C.E., part of the Chachapoya culture (same source as above):
"Anzick-1": boy from the Clovis culture in Park County, Montana, U.S.A. about 12,500 years ago, from "The Genome of a Late Pleistocene Human from a Clovis Burial Site in Western Montana" by Morten Rasmussen, et al. in Nature 506 (February 13, 2014): pages 225-229:
Carlos D. Bustamante, a professor of genetics at Stanford University in Stanford, California, U.S.A., has gathered additional Amerindian samples to try to find out which specific tribes contributed to a person's autosomal DNA.
His test isn't yet available at any direct-to-consumer lab. Bustamante's lab says samples will be collected later from the public – but not yet – but if you contact them using the web survey on their website they will get back to you later. I believe you should only contact them if you have a high amount of Amerindian ancestry.
Below are autosomal admixture results for celebrities who have had their autosomal DNA analyzed by Bustamante's lab on PBS's Finding Your Roots television show:
SANDRA CISNEROS (a writer with Mexican roots) in season 3, episode "The Pioneers":
MARK ALBA (Mexican roots), the father of the actress JESSICA ALBA, in season 2, episode "Decoding Our Past Through DNA":