Genetic history of indigenous peoples of the Americas
The genetic history of Indigenous peoples of the Americas (also named Amerindians or Amerinds in physical anthropology) is divided into two sharply distinct episodes: the initial peopling of the Americas during about 20,000 to 14,000 years ago (20–14 kya), and European contact, after about 500 years ago. The former is the determinant factor for the number of genetic lineages, zygosity mutations and founding haplotypes present in today's Indigenous Amerindian populations.
Most Amerindians groups are derived from a basal Ancestral lineage, which formed in Siberia prior to the Last Glacial Maximum, between about 36,000 and 25,000 years ago, from a combination of Proto-Mongoloid and Ancient North Eurasian ancestry and which dispersed throughout the Americas after about 16,000 years ago (an exception are the Na Dene and Eskimo–Aleut speaking groups, which are partially derived from Siberian populations which entered the Americas at a later time).
In the early 2000s, archaeogenetics was primarily based on Human Y-chromosome DNA haplogroups and Human mitochondrial DNA haplogroups. Autosomal "atDNA" markers are also used, but differ from mtDNA or Y-DNA in that they overlap significantly.
Analyses of genetics among Amerindian and Siberian populations have been used to argue for early isolation of founding populations on Beringia and for later, more rapid migration from Siberia through Beringia into the New World. The microsatellite diversity and distributions of the Y lineage specific to South America indicates that certain Amerindian populations have been isolated since the initial colonization of the region. The Na-Dené, Inuit and Indigenous Alaskan populations exhibit Haplogroup Q-M242; however, they are distinct from other indigenous Amerindians with various mtDNA and atDNA mutations. This suggests that the peoples who first settled in the northern extremes of North America and Greenland derived from later migrant populations than those who penetrated farther south in the Americas. Linguists and biologists have reached a similar conclusion based on analysis of Amerindian language groups and ABO blood group system distributions.
Genetic diversity and population structure in the American landmass is also measured using autosomal (atDNA) micro-satellite markers genotyped; sampled from North, Central, and South America and analyzed against similar data available from other indigenous populations worldwide. The Amerindian populations show a lower genetic diversity than populations from other continental regions. Observed is a decreasing genetic diversity as geographic distance from the Bering Strait occurs, as well as a decreasing genetic similarity to Siberian populations from Alaska (the genetic entry point). Also observed is evidence of a higher level of diversity and lower level of population structure in western South America compared to eastern South America. There is a relative lack of differentiation between Mesoamerican and Andean populations, a scenario that implies that coastal routes were easier for migrating peoples (more genetic contributors) to traverse in comparison with inland routes.
The over-all pattern that is emerging suggests that the Americas were colonized by a small number of individuals (effective size of about 70), which grew by a factor of 10 over 800 – 1000 years. The data also shows that there have been genetic exchanges between Asia, the Arctic, and Greenland since the initial peopling of the Americas.
Moreno-Mayar et al. (2018) have identified a basal Ancestral Native American (ANA) lineage. This lineage formed by admixture of early East Asian and Ancient North Eurasian lineages prior to the Last Glacial Maximum, ca. 36–25 kya. Basal ANA diverged into an "Ancient Beringian" (AB) lineage at ca. 20 kya. The non-AB lineage further diverged into "Northern Native American" (NNA) and "Southern Native American" (SNA) lineages between about 17.5 and 14.6 kya. Most pre-Columbian lineages are derived from NNA and SNA, except for the American Arctic, where there is evidence of later (after 10kya) admixture from Paleo-Siberian lineages.
In 2014, the autosomal DNA of a 12,500+-year-old infant from Montana was sequenced. The DNA was taken from a skeleton referred to as Anzick-1, found in close association with several Clovis artifacts. Comparisons showed strong affinities with DNA from Siberian sites, and virtually ruled out that particular individual had any close affinity with European sources (the "Solutrean hypothesis"). The DNA also showed strong affinities with all existing Amerindian populations, which indicated that all of them derive from an ancient population that lived in or near Siberia, the Upper Palaeolithic Mal'ta population.
According to an autosomal genetic study from 2012, Native Americans descend of at least three main migrant waves from East Asia. Most of it is traced back to a single ancestral population, called 'First Americans'. However, those who speak Inuit languages from the Arctic inherited almost half of their ancestry from a second East Asian migrant wave. And those who speak Na-dene, on the other hand, inherited a tenth of their ancestry from a third migrant wave. The initial settling of the Americas was followed by a rapid expansion southwards, by the coast, with little gene flow later, especially in South America. One exception to this are the Chibcha speakers, whose ancestry comes from both North and South America. 
Two 2015 autosomal DNA genetic studies confirmed the Siberian origins of the Natives of the Americas. However an ancient signal of shared ancestry with Australasians (Natives of Australia, Melanesia and the Andaman Islands) was detected among the Natives of the Amazon region. The migration coming out of Siberia would have happened 23,000 years ago.
A "Central Siberian" origin has been postulated for the paternal lineage of the source populations of the original migration into the Americas.
Q-M242 (mutational name) is the defining (SNP) of Haplogroup Q (Y-DNA) (phylogenetic name). Within the Q clade, there are 14 haplogroups marked by 17 SNPs.2009 In Eurasia, haplogroup Q is found among indigenous Siberian populations, such as the modern Chukchi and Koryak peoples. In particular, two groups exhibit large concentrations of the Q-M242 mutation, the Ket (93.8%) and the Selkup (66.4%) peoples. The Ket are thought to be the only survivors of ancient wanderers living in Siberia. Their population size is very small; there are fewer than 1,500 Ket in Russia.2002 The Selkup have a slightly larger population size than the Ket, with approximately 4,250 individuals.
Starting the Paleo-Indians period, a migration to the Americas across the Bering Strait (Beringia) by a small population carrying the Q-M242 mutation took place. A member of this initial population underwent a mutation, which defines its descendant population, known by the Q-M3 (SNP) mutation. These descendants migrated all over the Americas.
Haplogroup Q-M3 is defined by the presence of the rs3894 (M3) (SNP). The Q-M3 mutation is roughly 15,000 years old as that is when the initial migration of Paleo-Indians into the Americas occurred. Q-M3 is the predominant haplotype in the Americas, at a rate of 83% in South American populations, 50% in the Na-Dené populations, and in North American Eskimo-Aleut populations at about 46%. With minimal back-migration of Q-M3 in Eurasia, the mutation likely evolved in east-Beringia, or more specifically the Seward Peninsula or western Alaskan interior. The Beringia land mass began submerging, cutting off land routes.
Since the discovery of Q-M3, several subclades of M3-bearing populations have been discovered. An example is in South America, where some populations have a high prevalence of (SNP) M19 which defines subclade Q-M19. M19 has been detected in (59%) of Amazonian Ticuna men and in (10%) of Wayuu men. Subclade M19 appears to be unique to South American Indigenous peoples, arising 5,000 to 10,000 years ago. This suggests that population isolation and perhaps even the establishment of tribal groups began soon after migration into the South American areas. Other American subclades include Q-L54, Q-Z780, Q-MEH2, Q-SA01, and Q-M346 lineages. In Canada, two other lineages have been found. These are Q-P89.1 and Q-NWT01.
The principal-component analysis suggests a close genetic relatedness between some North American Amerindians (the Chipewyan and the Cheyenne) and certain populations of central/southern Siberia (particularly the Kets, Yakuts, Selkups and Altays), at the resolution of major Y-chromosome haplogroups. This pattern agrees with the distribution of mtDNA haplogroup X, which is found in North America, is absent from eastern Siberia, but is present in the Altais of southern central Siberia. Similarly, the Asian populations closest to Native Americans are characterized by a predominance of lineage P-M45* and low frequencies of C-RPS4Y.
Haplogroup R1 (Y-DNA) (specifically R1b) is the second most predominant Y haplotype found among indigenous Amerindians after Q (Y-DNA). The distribution of R1 is believed by some to be associated with the re-settlement of Eurasia following the last glacial maximum. One theory put forth is that R1 entered the Americas with the initial founding population, suggesting prehistoric Amerindian immigration from Asia through Beringia and correlating mostly with the frequency of haplogroups Q-M3 and P-M45*. A second theory is that it was introduced during European colonization. R1 is very common throughout all of Eurasia except East Asia and Southeast Asia. R1 (M173) is found predominantly in North American groups like the Ojibwe (50-79%), Seminole (50%), Sioux (50%), Cherokee (47%), Dogrib (40%) and Tohono O'odham (Papago) (38%).
A study of Raghavan et al. 2013 found that autosomal evidence indicates that skeletal remain of a south-central Siberian child carrying R* y-dna (Mal'ta boy-1) "is basal to modern-day western Eurasians and genetically closely related to modern-day Amerindians, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought." Sequencing of another south-central Siberian (Afontova Gora-2) revealed that "western Eurasian genetic signatures in modern-day Amerindians derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans." It is further theorized if "Mal'ta might be a missing link, a representative of the Asian population that admixed both into Europeans and Native Americans."
Haplogroup C-M217 is mainly found in indigenous Siberians, Mongolians and Kazakhs. Haplogroup C-M217 is the most widespread and frequently occurring branch of the greater (Y-DNA) haplogroup C-M130. Haplogroup C-M217 descendant C-P39 is commonly found in today's Na-Dené speakers, with the highest frequency found among the Athabaskans at 42%. This distinct and isolated branch C-P39 includes almost all the Haplogroup C-M217 Y-chromosomes found among all indigenous peoples of the Americas. The Na-Dené groups are also unusual among indigenous peoples of the Americas in having a relatively high frequency of Q-M242 (25%).
Some researchers feel that this may indicate that the Na-Dené migration occurred from the Russian Far East after the initial Paleo-Indian colonization, but prior to modern Inuit, Inupiat and Yupik expansions.
The common occurrence of the mtDNA Haplogroups A, B, C, and D among eastern Asian and Amerindian populations has long been recognized, along with the presence of Haplogroup X. As a whole, the greatest frequency of the four Amerindian associated haplogroups occurs in the Altai-Baikal region of southern Siberia. Some subclades of C and D closer to the Amerindian subclades occur among Mongolian, Amur, Japanese, Korean, and Ainu populations.
When studying human mitochondrial DNA (mtDNA) haplogroups, the results indicated until recently[year needed] that Indigenous Amerindian haplogroups, including haplogroup X, are part of a single founding East Asian population. It also indicates that the distribution of mtDNA haplogroups and the levels of sequence divergence among linguistically similar groups were the result of multiple preceding migrations from Bering Straits populations. All indigenous Amerindian mtDNA can be traced back to five haplogroups, A, B, C, D and X. More specifically, indigenous Amerindian mtDNA belongs to sub-haplogroups A2, B2, C1b, C1c, C1d, D1, and X2a (with minor groups C4c, D2a, and D4h3a). This suggests that 95% of Indigenous Amerindian mtDNA is descended from a minimal genetic founding female population, comprising sub-haplogroups A2, B2, C1b, C1c, C1d, and D1. The remaining 5% is composed of the X2a, D2a, C4c, and D4h3a sub-haplogroups.
X is one of the five mtDNA haplogroups found in Indigenous Amerindian peoples. Unlike the four main American mtDNA haplogroups (A, B, C and D), X is not at all strongly associated with east Asia. Haplogroup X genetic sequences diverged about 20,000 to 30,000 years ago to give two sub-groups, X1 and X2. X2's subclade X2a occurs only at a frequency of about 3% for the total current indigenous population of the Americas. However, X2a is a major mtDNA subclade in North America; among the Algonquian peoples, it comprises up to 25% of mtDNA types. It is also present in lower percentages to the west and south of this area — among the Sioux (15%), the Nuu-chah-nulth (11%–13%), the Navajo (7%), and the Yakama (5%). Haplogroup X is more strongly present in the Near East, the Caucasus, and Mediterranean Europe. The predominant theory for sub-haplogroup X2a's appearance in North America is migration along with A, B, C, and D mtDNA groups, from a source in the Altai Mountains of central Asia.
Sequencing of the mitochondrial genome from Paleo-Eskimo remains (3,500 years old) are distinct from modern Amerindians, falling within sub-haplogroup D2a1, a group observed among today's Aleutian Islanders, the Aleut and Siberian Yupik populations. This suggests that the colonizers of the far north, and subsequently Greenland, originated from later coastal populations. Then a genetic exchange in the northern extremes introduced by the Thule people (proto-Inuit) approximately 800–1,000 years ago began. These final Pre-Columbian migrants introduced haplogroups A2a and A2b to the existing Paleo-Eskimo populations of Canada and Greenland, culminating in the modern Inuit.
A 2013 study in Nature reported that DNA found in the 24,000-year-old remains of a young boy from the archaeological Mal'ta-Buret' culture suggest that up to one-third of indigenous Americans' ancestry can be traced back to western Eurasians, who may have "had a more north-easterly distribution 24,000 years ago than commonly thought" "We estimate that 14 to 38 percent of Amerindian ancestry may originate through gene flow from this ancient population," the authors wrote. Professor Kelly Graf said,
"Our findings are significant at two levels. First, it shows that Upper Paleolithic Siberians came from a cosmopolitan population of early modern humans that spread out of Africa to Europe and Central and South Asia. Second, Paleoindian skeletons like Buhl Woman with phenotypic traits atypical of modern-day indigenous Americans can be explained as having a direct historical connection to Upper Paleolithic Siberia."
A route through Beringia is seen as more likely than the Solutrean hypothesis. An abstract in a 2012 issue of the "American Journal of Physical Anthropology" states that "The similarities in ages and geographical distributions for C4c and the previously analyzed X2a lineage provide support to the scenario of a dual origin for Paleo-Indians. Taking into account that C4c is deeply rooted in the Asian portion of the mtDNA phylogeny and is indubitably of Asian origin, the finding that C4c and X2a are characterized by parallel genetic histories definitively dismisses the controversial hypothesis of an Atlantic glacial entry route into North America."
Another study, also focused on the mtDNA (that which is inherited through only the maternal line), revealed that the indigenous people of the Americas have their maternal ancestry traced back to a few founding lineages from East Asia, which would have arrived via the Bering strait. According to this study, it is probable that the ancestors of the Native Americans would have remained for a time in the region of the Bering Strait, after which there would have been a rapid movement of settling of the Americas, taking the founding lineages to South America.
According to a 2016 study, focused on mtDNA lineages, "a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages".
There is genetic evidence for an early wave of migration to the Americas. It is uncertain whether this "Paleoamerican" (also "Paleoamerind", not to be confused with the term Paleo-Indian used of the early phase of Amerinds proper) migration took place in the early Holocene, thus only shortly predating the main Amerind peopling of the Americas, or whether it may have reached the Americas substantially earlier, before the Last Glacial Maximum. Genetic evidence for "Paleoamerinds" consists of the presence of apparent admixture of archaic Sundadont lineages to the remote populations in the South American rain forest, and in the genetics and cranial morphology of Patagonians-Fuegians. Nomatto et al. (2009) proposed into Beringia occurred between 40k and 30k cal years BP, with a pre-LGM migration into the Americas followed by isolation of the northern population following closure of the ice-free corridor. Evidence of people from Australia and Melanesia admixture in Amazonian populations was found by Skoglund and Reich (2016).
Archaeological evidence for pre-LGM human presence in the Americas was first presented in the 1970s. notably the "Luzia Woman" skull found in Brazil and the Monte Verde site in Chile, both discovered in 1975. Other notable sites of early human inhabitation found in North America include Paisley Caves, Oregon and Bluefish Caves, Canada.
Old World genetic admixtureEdit
South and Central AmericaEdit
In Latin America in particular, significant racial admixture took place between the indigenous Amerind population, the European-descended colonial population, and the Sub-Saharan African populations imported as slaves. From about 1700, a Latin American terminology developed to refer to the various combinations of mixed racial descent produced by this.
Many individuals who self-identify as one race exhibit genetic evidence of a multiracial ancestry. The European conquest of South and Central America, beginning in the late 15th century, was initially executed by male soldiers and sailors from the Iberian Peninsula (Spain and Portugal).[unreliable source] The new soldier-settlers fathered children with Amerindian women and later with African slaves.[unreliable source] These mixed-race children were generally identified by the Spanish colonist and Portuguese colonist as "Castas".
The North American fur trade during the 16th century brought many more European men, from France, Ireland, and Great Britain, who took North Amerindian women as wives. Their children became known as "Métis" or "Bois-Brûlés" by the French colonists and "mixed-bloods", "half-breeds" or "country-born" by the English colonists and Scottish colonists.
Native Americans in the United States are more likely than any other racial group to practice racial exogamy, resulting in an ever-declining proportion of indigenous ancestry among those who claim a Native American identity. In the United States 2010 census, nearly 3 million people indicated that their race was Native American (including Alaska Native). This is based on self-identification, and there are no formal defining criteria for this designation. Especially numerous was the self-identification of Cherokee ethnic origin, a phenomenon dubbed the "Cherokee Syndrome." The context is the cultivation of an opportunistic ethnic identity related to the perceived prestige associated with Native American ancestry. Native American identity in the Eastern United States is mostly detached from genetic descent, and embraced by people of predominantly European ancestry. Some tribes have adopted criteria of racial purity, usually through a Certificate of Degree of Indian Blood, and practice disenrollment of tribal members unable to provide proof of Native American ancestry. This topic has become a contentious issue in Native American reservation politics,
Recent archaeological findings in Alaska have shed light on the existence of a previously unknown Native American population that has been academically named "Ancient Beringians." Although it is popularly agreed among archeologists that early settlers had crossed into Alaska from Russia through the Bering Strait land bridge, the issue of whether or not there was one founding group or several waves of migration is a controversial and prevalent debate among academics in the field today. In 2018, the sequenced DNA of a native girl, whose remains were found at the Sun River archaeological site in Alaska in 2013 (maybe add citation here), proved not to match the two recognized branches of Native Americans and instead belonged to the early population of Ancient Beringians. This breakthrough is said to be the first direct genomic evidence that there was potentially only one wave of migration in the Americas that occurred, with genetic branching and division transpiring after the fact. The migration wave is estimated to have emerged about 20,000 years ago. The Ancient Beringians are said to be a common ancestral group among contemporary Native American populations today, which differs in results collected from previous research that suggests that modern populations were ancestors of either Northern and Southern branches. Experts were also able to use wider genetic evidence to establish that the split between the Northern and Southern American branches of civilization from the Ancient Beringians in Alaska only occurred about 17,000 and 14,000 years, further challenging the concept of multiple migration waves occurring during the very first stages of settlement.
Prior to the 1952 confirmation of DNA as the hereditary material by Alfred Hershey and Martha Chase, scientists used blood proteins to study human genetic variation. The ABO blood group system is widely credited to have been discovered by the Austrian Karl Landsteiner, who found three different blood types in 1900. Blood groups are inherited from both parents. The ABO blood type is controlled by a single gene (the ABO gene) with three alleles: i, IA, and IB.
Research by Ludwik and Hanka Herschfeld during World War I found that the frequencies of blood groups A, B and O differed greatly from region to region. The "O" blood type (usually resulting from the absence of both A and B alleles) is very common around the world, with a rate of 63% in all human populations. Type "O" is the primary blood type among the indigenous populations of the Americas, in-particular within Central and South America populations, with a frequency of nearly 100%. In indigenous North American populations the frequency of type "A" ranges from 16% to 82%. This suggests again that the initial Amerindians evolved from an isolated population with a minimal number of individuals.
The standard explanation for such a high population of Native Americans with blood type O comes from the idea of Genetic drift, in which the small nature of Native American populations meant the almost complete absence of any other blood gene being passed down through generations. Other related explanations include the Bottleneck explanation which states that there were high frequencies of blood type A and B among Native Americans but severe population decline during the 1500s and 1600s caused by the introduction of disease from Europe resulted in the massive death toll of those with blood types A and B. Coincidentally, a large amount of the survivors were type O.
European diseases and genetic modificationEdit
A team led by Ripan Malhi, an anthropologist at the University of Illinois in Urbana, conducted a study where they used a scientific technique known as whole exam sequencing to test immune-related gene variants within native americans. Through analyzing ancient and modern native DNA, it was found that HLA-DQA1, a variant gene that codes for protein in charge of differentiating between healthy cells from invading viruses and bacteria were present in nearly 100% of ancient remains but only 36% in modern Native Americans. These finding suggest that European-borne epidemics such as smallpox altered the disease landscape of the Americas, leaving survivors of these outbreaks less likely to carry variants like HLA-DQA1. This made them less able to cope with new diseases. The change in genetic makeup is measured by scientists to have occurred around 175 years ago, during a time when the smallpox epidemic was ranging through the Americas.
|PEOPLE GROUP||O (%)||A (%)||B (%)||AB (%)|
|Blackfoot Confederacy (N. American Indian)||17||82||0||1|
|Inuit (Eastern Canada & Greenland)||54||36||23||8|
|Hawaiians (Polynesians, non-Amerindian)||37||61||2||1|
|Indigenous North Americans (as a whole Native Nations/First Nations)||79||16||4||1|
|Wikimedia Commons has media related to Genetic studies of indigenous populations of the Americas.|
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