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A language map with color. Branch lengths are scaled according to genetic distance, but for ease of visualization, a different scale is used on the left and right sides of the middle tick mark at the bottom of the figure. The tree was rooted along the branch connecting the Siberian populations and the Native American populations, and for convenience, the forced bootstrap score of 100% for this rooting is indicated twice. In the neighbor-joining tree, a reasonably well-supported cluster (86%) includes all non-Andean South American populations, together with the Andean-speaking Inga population from southern Colombia. Within this South American cluster, strong support exists for separate clustering of Chibchan–Paezan (97%) and Equatorial–Tucanoan (96%) speakers (except for the inclusion of the Equatorial–Tucanoan Wayuu population with its Chibchan–Paezan geographic neighbors, and the inclusion of Kaingang, the single Ge–Pano–Carib population, with its Equatorial–Tucanoan geographic neighbors). Within the Chibchan–Paezan and Equatorial–Tucanoan subclusters several subgroups have strong support, including Embera and Waunana (96%), Arhuaco and Kogi (100%), Cabecar and Guaymi (100%), and the two Ticuna groups (100%). When the tree-based clustering is repeated with alternate genetic distance measures, despite the high Mantel correlation coefficients between distance matrices (0.98, 0.98, and 0.99 for comparisons of the Nei and Reynolds matrices, the Nei and chord matrices, and the Reynolds and chord matrices, respectively), higher-level groupings tend to differ slightly or to have reduced bootstrap support.
A genetic tree showing some neighbour-joining relationships within Amerindian populations.

Indigenous Amerindian genetics primarily focus on Human Y-chromosome DNA haplogroups and Human mitochondrial DNA haplogroups. "Y-DNA" is passed solely along the patrilineal line, from father to son, while "mtDNA" is passed down the matrilineal line, from mother to offspring of both sexes. Neither recombines, and thus Y-DNA and mtDNA change only by chance mutation at each generation with no intermixture between parents' genetic material.[1] Autosomal "atDNA" markers are also used, but differ from mtDNA or Y-DNA in that they overlap significantly.[2] AtDNA is generally used to measure the average continent-of-ancestry genetic admixture in the entire human genome and related isolated populations.[2]

The genetic pattern indicates Indigenous Amerindians experienced two very distinctive genetic episodes; first with the initial peopling of the Americas, and secondly with European colonization of the Americas.[3][4] The former is the determinant factor for the number of gene lineages, zygosity mutations and founding haplotypes present in today's Indigenous Amerindian populations.[3]

Human settlement of the New World occurred in stages from the Bering sea coast line, with an initial 15,000 to 20,000-year layover on Beringia for the small founding population.[5][6][7] The micro-satellite 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.[8] The Na-Dené, Inuit and Indigenous Alaskan populations exhibit haplogroup Q (Y-DNA); however, they are distinct from other indigenous Amerindians with various mtDNA and atDNA mutations.[9][10][11] This suggests that the earliest migrants into the northern extremes of North America and Greenland derived from later migrant populations.[12][13]

Contents

Introduction

The X and Y human chromosomes are thought to have originated from a pair of identical chromosomes[14] (300 - 166 million years ago[15][16][17]), termed Allosome, when an ancient ancestral mammal developed an allelic variation, a so-called 'sex locus' - simply possessing this allele caused the organism to be male.[18] The chromosome with this allele became the Y chromosome, while the other member of the pair became the X chromosome. Over time, genes which were beneficial for males and harmful to (or had no effect on) females developed specifically on the Y chromosome, or were acquired through the process of translocation.[19] Because the Y chromosome is passed down exclusively from father to son, all male humans (Y chromosomes) today trace back to a single prehistoric father termed "Y chromosomal Adam" originating from Africa.[20] The Y chromosome spans about 60 million base pairs (the building blocks of DNA) and represents about 2 percent of the total DNA in all human cells.[21] The original "Y chromosomal Adam" DNA sequencing has mutated rarely over the 20,000 generations, but each time a new mutation occurs there is a new branch in a haplogroup resulting in a new subclade.[22] MtDNA mutations are also passed down relatively unchanged from generation to generation; so all humans share the same mtDNA-types, the logical extension of this is that all humans ultimately trace back to one woman, who is commonly referred to as Mitochondrial Eve.[23][24] Both females and males inherit their Mitochondrial DNA (mtDNA) only from their mother.[25] This line of biological inheritance, therefore, stops with each male.[26] Consequently, Y-DNA is more commonly used by the general public for tracing genetic heritage.[26][27][28]

An autosome (atDNA) is a chromosome that is not a sex chromosome – that is to say there are an equal number of copies of the chromosome in males and females.[2] Autosomal DNA testing is generally used to determine the "genetic percentages" of a person's ancestry from particular continents/regions or to identify the countries and "tribes" of origin on an overall basis. Genetic admixture tests arrive at these percentages by examining single-nucleotide polymorphism (SNP), which are locations on the DNA where one nucleotide has "mutated" or "switched" to a different nucleotide.[2] One way to examine the support for particular colonization routes within the American landmass is to determine if a closer relationship between zygosity and geography is observed when “effective” geographic distances are computed along these routes, rather than along shortest-distance paths.[29]

Y-DNA

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Parent clade

Q-M242 (mutational name) is the defining (SNP) of Haplogroup Q (Y-DNA) (phylogenetic name).[8] Within the Q clade, there are 14 haplogroups marked by 17 SNPs.2009[30][31] In Eurasia haplogroup Q-M2 is found among Siberian populations, in particular two populations, the Kets (93.8%) and the Selkups (66.4%).[32] The Kets are thought to be the only survivors of ancient nomads living in Siberia.[5] Their population size is very small; there a fewer then 1,500 Kets in Russia.2002[5] The Selkups have a slightly larger population size than the Kets, with approximately 4,250 individuals. 2002[8] Starting the lithic stage; a migration to the Americas across the Bering Strait (Beringia), was done by a small Chukchi Indigenous population with the Q-M242 mutation.[33][34] A member of this initial "Chukchi"[35] population underwent a mutation, producing its descendant population defined by the Q-M3 (SNP) mutation that migrated all over the Americans.[30]

Subclades

Dr. Peter Underhill and his colleagues at Stanford University first discovered the indigenous Amerindian (SNP), that was to become known as Haplogroup Q1a3a (Y-DNA) and/or Q-M3.[3][5] Haplogroup Q1a3a is defined by the presence of the rs3894 (M3) single nucleotide polymorphism (SNP).[8] The Q-M3 mutation is roughly 10,000 to 15,000 years old as the initial migration of Paleo-Indians into the Americas occurred.[7][36] Q-M3 is the predominate haplotype in the Americas at a rate of (58%) in South American populations, (50%) in the Na-Dené populations, and in the North American Arctic populations at (46%).[32] 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, as the Beringia land mass began submerging, cutting off land routes.[6][32][37]

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 M19.[38] M19 has been detected in (59%) of Amazonian Ticuna men and in (10%) of Wayuu men.[38] Subclade M19 appears to be unique to South American Indigenous peoples arising 5,000 to 10,000 years ago.[38] Implying that population isolation and perhaps even the establishment of tribes began soon after migration into the South American areas.[5][39]

Y-DNA Q haplogroup tree

  • Y-chromosomal Adam - when analyzing the Y-chromosome DNA from males in all regions of the world, geneticists have concluded that all humans alive today are patrilineally descended from a single man who lived in Africa around 60,000 to 90,000 years ago.[40][41][42][43]
    • BT- and A haplogroups originated 50,000 to 60,000 years ago, within the Horn of Africa from Y-chromosomal Adam. BT is still found among hunter-gatherer groups in Ethiopia and Sudan, its also seen among click language-speaking populations.[44][45]
      • CT - represents the most recent common male ancestor to the majority of men alive today.[46] Believed to pre-date the "out of Africa" migration of anatomically modern humans.[46] CT is therefore the ancestral male lineage of most men in Africa, where haplogroup E is most common, and non Africans, where haplogroup F is dominant.[46]
        • CF - the haplogroup is hypothetical because no male in haplogroup CF* has yet been discovered.2008 As its compound name implies, its the ancestral haplogroup to both Haplogroup C and the much larger Haplogroup F.[47]
          • F - this ancient haplogroup first appeared in India, the Levant, or the Arabian Peninsula 50,000 to 55,000 years ago: 50,300±6500, Hammer and Zegura 2002; 48,000(38,700-55,700)[43] The groups descending from haplogroup F are found in 90% of the worlds current male population, excluding most of the Sub-Saharan African and sub-regions of the Oceanias.[48]
            • IJK - K is also a vast lineage found in northern Eurasia, eastern Eurasia, Melanesia, with a moderate distribution in southeast Asia, northern Africa, and among Oceanic populations.[49] Haplogroup K decedents encompass haplogroups T, L, MNOPS.[49]
              • MNOPS - P mutation is believed to have arisen north of the Hindu Kush, in Siberia, Kazakhstan, or Uzbekistan, approximately 35,000 to 45,000 years ago.[50] P is rarely found as an undifferentiated haplogroup today, however its the ancestral source for both haplogroup Q and the much larger haplogroup R.[50]
                • Q (M242) - Origin: - Krasnoyarsk Krai or Sakha Republic, approximately 18,000 to 23,000 years ago[8][51]
                  • Q* - found at low frequencies in India and Pakistan[30][32]
                  • Q1 (P36.2)
                    • Q1*
                    • Q1a (MEH2)
                      • Q1a* - 4000-year-old human remains of a Saqqaq individual belonged to this haplogroup.[52]
                      • Q1a1 (M120, M265/N14) - found at low frequency among Chinese, Koreans, Dungans, Hazara, and Tibetans[53][54]
                      • Q1a2 (M25, M143) - found at low to moderate frequency among some populations of Southwest Asia, Central Asia, and Siberia
                      • Q1a3 (M346)
                        • Q1a3* - found at low frequency in Pakistan, India, and Tibet[32]
                        • Q1a3a (M3) - subclade associated with all Indigenous peoples of the Americas. Origin: Americas 10,000 to 15,000 years ago[32][51]
                           : 10,000 year old human remains discovered in Alaska are part of this subclade[55]
                          • Q1a3a*
                          • Q1a3a1 (M19) - subclade found among Indigenous South Americas, such as the Ticuna and the Wayuu.[51]
                            - Origin: South America approximately 5,000 to 10,000 years ago[30][31][32]
                          • Q1a3a2 (M194) - this is the defining mutation for Q1a3a2. It has only been found in South American populations[51]
                          • Q1a3a3 (M199, P106, P292 aka M320) - subclades that have only been found in South American populations[8][30]

Subclade C3b

Map of the Americas with two different lines showing two separate genetic populations entering the New world, via the Bering Sea down the west coast of the continent
Time scale of Q (M3) haplogroup migrating in the Americas , with a separate entry of C3 haplogroup

Haplogroup C3 (M217, P44) is mainly found in indigenous Siberians, Mongolians and Oceanic populations. Haplogroup C3 is the most widespread and frequently occurring branch of the greater (Y-DNA) haplogroup C. Haplogroup C3 is believed to have originated approximately 20,000 years before present in eastern or central Asia. Haplogroup C3 decedent C3b (P39) is commonly found among today's Na-Dené speakers. This distinct and isolated branch C3b (P39) includes almost all the Haplogroup C3 Y-chromosomes found among any indigenous peoples of the Americas.[56] The Na-Dené groups are also unusual among indigenous peoples of the Americas in having a relatively high frequency of Q-M242 (25%).[32] This implies that the Na-Dené migration occurred from the Russian Far East; after the initial Paleo-Indians colonization, but prior to modern Inuit, Inupiat and Yupik expansions.[9][13]

* Note: (One particular haplotype within the Y-DNA Haplogroup C3 has received a great deal of attention for the possibility that it may represent direct patrilineal Descent from Genghis Khan. Genghis Y-chromosomal lineage is present in about 8% of the men in a large region of Asia and about 0.5% of the men in the world (Khan haplotype "C3c" is found lower on the C tree and is not found in Indigenous Americas.[66])

MtDNA

Schematic illustration of maternal geneflow in and out of Beringia.Colours of the arrows correspond to approximate timing of the events and are decoded in the coloured time-bar. The initial peopling of Berinigia (depicted in light yellow) was followed by a standstill after which the ancestors of indigenous Americans spread swiftly all over the New World while some of the Beringian maternal lineages–C1a-spread westwards. More recent (shown in green) genetic exchange is manifested by back-migration of A2a into Siberia and the spread of D2a into north-eastern America that post-dated the initial peopling of the New World.
Schematic illustration of maternal (mtDNA) gene-flow in and out of Beringia, from 25,000 years ago to present.

Mitochondrial Eve - is defined as the woman who was the "matrilineal" most recent common ancestor for all current living humans. Mitochondrial Eve is generally estimated to have lived around 200,000 years ago most likely in East Africa, long before her male counterpart Y-chromosomal Adam.[67] Mitochondrial Eve is the most recent common matrilineal ancestor, not the most recent common ancestor (MRCA).[68][69] When studying 86 complete mitochondrial genomes the results conclude that all Indigenous Amerindian haplogroups, including Haplogroup X (mtDNA), are part of a single founding east Asian population.[70] It also indicates that the distribution of Mitochondrial DNA (mtDNA) haplogroups and the levels of sequence divergence among linguistically similar groups, were the result of proceeding multiple migrations from Bering Straits populations.[25][71] All Indigenous Amerindians mtDNA can be traced back to five haplogroups types A, B, C, D and X.[72] More specifically, Indigenous Amerindians mtDNA belongs to sub-haplogroups that are unique to the Americas and not found in Asia or Europe: A2, B2, C1, D1, and X2a (with minor groups C4c, D2, D3, and D4h3).[71] This suggests that 95% of Indigenous Amerindians mtDNAs are descended from a minimal genetic founding female population, comprising of sub-haplogroups A2, B2, C1b, Cc, C1d, and D1.[72] The remaining 5% is composed of the X2a, D2, D3, C4, and D4h3 sub-haplogroups.[71][72]

X (mtDNA) is one of the five mtDNA -haplogroups found in Amerindian indigenous peoples. Curiously, unlike the four main American mtDNA-haplogroups (A, B, C and D) - X is not at all strongly associated with east Asia.[5] Haplogroup X (mtDNA) genetic sequences diverged about 20,000 to 30,000 years ago to give two sub-groups, X1 and X2. X2's subclad X2a occurs only at a frequency of about 3% for the total current indigenous population of the Americas.[5] However, X2a is a major mtDNA subclade in North America, where among the Algonquian peoples it comprises up to 25% of mtDNA types.[3][73] It is also present in lesser 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%).[33] The (mtDNA)X-haplo is more strongly present in the Near East, the Caucasus, and Mediterranean Europe.[33] The predominate theory for haplogroup X (subclade X2a) appearance in North America is migration along with A,B,C, and D mtDNA groups; from a matrilineal ancestral source, originating in the Altai Region of central Asia.[74]

Sequencing of mitochondrial genome from Paleo-Eskimo remains (3,500 years old) are distinct from modern Amerindians; falling within haplogroup (mtDNA) D2a1, a group observed among today's Aleutian Islanders the Aleuts and Siberian Yupik populations.[75] This suggests that the colonizers of the far north and subsequently Greenland, originated from later coastal populations.[75] Then a genetic exchange in the northern extremes introduced by the Thule people (proto-Inuit) approximately 800 - 1,000 years ago began.[11][76] This final migrants with (mtDNA) haplogroups A2a and A2b, interbred with the existing Paleo-Eskimo populations of Canada and Greenland, culminating as the modern Inuit.[11][76][77]

AtDNA

A map with five colored squares, depicting the genetic split between 18 different human groups of the world.
A genetic tree of 18 world human groups by a neighbour-joining autosomal relationships.

When examined genetic diversity and population structure in the American landmass using autosomal (atDNA) micro-satellite markers genotyped; sampled from North, Central, and South America, analyzed against similar data available from other indigenous populations worldwide.[29][78] The Amerindian populations show a lower genetic diversity and cellular differentiation than populations from other continental regions.[78] Observe is both decreasing genetic diversity as geographic distance from the Bering Strait occurs and of decreasing genetic similarity to Siberian populations from Alaska (genetic entry point).[29][78] Also observe is evidence of a higher level of diversity and lower level of population structure in western South America compared to eastern South America.[29][78] A relative lack of differentiation between Mesoamerican and Andean populations, a scenario that implies coastal routes were easier for migrating peoples (more genetic contributors) to traverse in comparison with inland routes.[29] The over all pattern that is emerging suggest that the Americas were recently colonized by a small number of individuals (effective size of about 70), and then grew by a factor of 10 rapidly.[5][79] The data also shows that there has been genetic exchanges between Asia, the Arctic and Greenland since the initial peopling of the Americas.[77][79]

Overlaps between DNA types

Populations that have a specific combination of autosome, Y-haplogroup and mt-haplogroup mutations can generally be found with regional variations. Autosomes, Y mutations and mt mutations do not necessarily occur at a similar time and there are differential rates of sexual selection between the two sex chromosomes.[80] Combined with the founder effect and genetic drift this can alter the genetic composition of isolated populations resulting in very distinguishable mutation patterns.[81] (i.e Taínos,[82] Fuegians,[83] Inuit,[84] Yupik[85] and Algonquian[5])

The rough overlaps between Y-DNA and mtDNA between the Americas, Circumpolar north, and Siberian indigenous populations are:

Y-DNA haplogroup(s) mtDNA haplogroup(s) Geographical area(s)
Q, C3 A, X, Y, C, D
(M types), (N types)
Russian far east, Americas, Arctic
A simulation image of mtDNA and Y-DNA overlaps in an isolate population. In this example 20 balls representing allele - 10 red and 10 blue are randomly changing in five clear jars, there is a shift from the red allele at a frequency of 50% to blue allele at a frequency 100% in just 5 generations.

Old world genetic admixture

Admixture triangle of five American ethnic groups[86]

The term "miscegenation" has been used since the 19th century to describe interracial marriage and interracial sex; and more generally to the process of racial admixture, which has taken place since ancient history, but has become more global through European colonialism since the Age of Discovery.[87] Miscegenation (genetic exchange) between two populations reduces the genetic distance between the populations and is measurable in DNA patterns.[80] During the Age of Discovery which began in the early 15th century, European explorers sailed the oceans eventually reaching all the major continents.[88] In the process they came into contact with many populations that had been isolated for thousands of years.[89] The genetic demographic composition of the old world has not changed significantly since the age of discovery. However, the new world genetic demographics were radically changed within a short time following the voyage of Christopher Columbus.[89] The European colonization of the Americas brought Amerindian populations into contact with the distant peoples of Europe, Africa and Asia. As a result many countries in the Americas today have significant and complex multiracial populations.[89] Furthermore many individuals who self-identify themselves by only one race still exhibit genetic evidence of a multiracial ancestry.[90]

The early conquest of Latin America was primarily carried out by male soldiers and sailors from Spain and Portugal historically termed "conquistadors".[91] Since they were not accompanied by European women on their journeys, this new settlers married and fathered children with Amerindian women and the later period female slaves displaced from Africa.[92] This new Latin American children were generally termed as Castas during the post-Conquest period.[93] The 17th century North American fur trade resulted in European men, mainly from France and Great Britain interbreeding with the Amerindian women of North American.[94] Their offspring were historically refers to as Métis, Bois-Brûlés, mixed-bloods, half-breeds, Acadian or Country-born.[95] Towards the end of the 19th Century and beginning of the 20th century large numbers of north Europeans began to migrate to South America and consequently altered the Latin American demographics once again.[96] Since World War II and the subsequent advancement in aviation, the current American populations genetic heritage can be traced to all corners of the world.[97][5]

Blood groups

A and B are codominant, giving the AB phenotype.

Prior to the discovery of DNA as the hereditary material, scientists used blood proteins to study human genetic variation.[98] The ABO blood group system is widely credited to have been discovered by the Austrian scientist Karl Landsteiner, who found three different blood types in 1900.[99] 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.[100]

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.[98] The O blood type (usually resulting from the absence of both A and B alleles) is very common around the world at a rate of 63% in all human populations.[101] Type O is very high in frequency among the indigenous populations of Central and South America at a rate of nearly 100%.[101] Among indigenous North American populations the frequency of type A is 31%, while among indigenous South Americans it is 4%.[101] Blood group O is the earliest blood group and dates to the Stone Age. This would suggest that the initial Amerindian population evolved in isolation with a minimal population number.[102] Blood groups of Inuit and Native Alaskan populations indicate migration from Asia accrued in stages after the initial wave of first settlers.[103]

See also

References

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