An Early Peopling of America (Part II)

An Early Peopling of America
This is the second part of an essay which summarizes in a neat way many things that I have posted on my blog.

Click here for Part I

An Early Peopling of America (Part II)

Austin V. Whittall

Abstract

The argument used against an ancient peopling of America -before c. 25 thousand years ago (Kya)- is that there were no modern humans in Northeastern Siberia at that time ready to cross Beringia and enter North America.
Another claim is that only then, during the final period of the Wisconsin glaciations, had modern humans acquired the know-how to be able to survive in such a hostile environment and that the sea level had dropped enough to allow entry.
However archaeological remains dating >30 Kya in the Americas and the in depth sequencing of modern and archaic genomes open up the possibility that the first human occupant of the New World may have been either Homo erectus or H. Neanderthalensis.
This overview will present the case for an early peopling of America by these hominids and a later admixture in America with modern H. sapiens, which defined the particular genetic lineages of the New World.

Genetic Evidence

Several genetic markers are found in America, Europe and Western Asia but are absent in Eastern Asia, the purported ancestral homeland of Amerindians, this supports the notion that the modern humans who initially peopled America were very different from the current inhabitants of Eastern Asia. Later migratory waves added East Asian elements to the original American population.

Furthermore, many genetic traits admixed from primitive hominids are found at the highest global frequencies in America, which would be the expected consequence if admixture had taken place in the Americas.

Bottlenecks and founder effects

Statistical analysis attributes the current lack of genetic diversity in the Americas to founder effects: Small founding populations in the initial peopling of the continent. These tiny groups purportedly contributed a large fraction of the ancestry of all contemporary Native Americans.

These studies overlook a unique situation which did not occur in other parts of the Old World: European discovery and conquest after 1492 AD provoked a massive eradication of native populations. This decreased the Amerindian gene pools dramatically (to between 33% and 4% of their original sizes). Over 80 M people died due to war and, mostly, microbia (measles, influenza, smallpox). Selective pressure acted to favor those better equipped to face the new environment.

It was this combination of disease and war-caused bottleneck plus natural selection that distorted the pre-Hispanic gene-frequency distribution obliterating genetic lineages, and obscuring ancestral frequency patterns. The pre-Hispanic genetic map of America was different and may have been much richer (i.e. similar to that of Asia or Austronesia). Studies that analyze gene frequencies in the New World do not seem to bear this in mind (1).

Common traits of East Asians and Native Americans

Some East Asian genetic markers are found in moderate frequencies among Amerindians. These could have entered the original American gene pool either recently during later peopling waves or, introgressed from archaic hominid populations that admixed with the H. sapiens that would become East Asians and Native Americans.

A remark on Northern North American natives (Aleuts, Na-Dene and Inuit). These groups share several traits with West Beringian populations suggesting a recent arrival in North America. Furthermore genetic analysis indicates that they cluster together in a distinct separate branch from all other Amerindian people (2).

Dental Shoveling

Dental shoveling appears in the earliest hominids and is found in Australopithecus, Neanderthal, H. erectus (3) and the Dmanisi hominins from Georgia, Caucasus (4). Modern humans are divided into two distinct regions with a global east-west gradient of decreasing shoveling. People belonging to Mongoloid groups (North Eastern Asians and, partially, American Indians) have the highest frequency of shoveled incisors while the rest of the world has chiseled ones (5).

This global cline is best explained by the replacement of H. erectus in west Eurasia by modern humans and their assimilation by admixture in East Asia (6).

Shoveling is caused by the Ectodysplasin receptor gene (EDAR), also associated with hair thickness and the size and quantity of sweat and mammary glands. It is frequent in Asian populations and absent in Europeans, Africans, Denisovans and the Mal'ta remains (more o Mal'ta below) who carry the ancestral allele (7)(8)(9). The mutation or introgression (admixed through direct contact with H. erectus) is believed to have appeared in central China >30 Kya (10)(11), a late date in our opinion since it was obtained by simulations restrained by a 15 Kya date for peopling America.

Os Inca

The archaic looking skull from Lovelock cave, Nevada, besides a Neanderthal-like occipital torus and prominent brow-ridge also exhibited another ancient trait: Os Inca (12). This morphological feature is found in fossil hominids (Australopithecus, Homo erectus, and archaic H. sapiens) and is very frequent in fossil and modern Chinese populations. Infrequent among Europeans and North East Asians (1.5 - 2%) it is quite common among North American Natives (6.5%), East Asians and Sub Saharan Africans (4.5%) (13).

Strong presence of Neanderthal admixture in America

Both of the preceding traits, shoveled incisors and Os Inca with specific geographical location in China and America could denote two separate admixture events in each of those regions. We rule out an East Asian admixture and later migration of admixed populations into America because other Chinese traits are absent in the New World and certain archaic features found in America are absent in East Asia indicating no outflow of those traits back towards Eastern Asia.

Furthermore, introgression may not only be due only to H. erectus, but also to Neanderthals who moved east from Central Asia expanding into China during MIS 3 times -29 to 58 Kya.(14), as attested by a high presence of Neanderthal ancestry in Eastern Asians (15) and even higher among Amerindians as suggested by the genome sequence of an Altai Mountain Neanderthal (16) and a PCA analysis (17).

Evidence from different genetic markers

B006 (ds44 gene)

B006 is the least derived haplotype of X chromosome’s dystrophin gene (ds44) and it is found in Neanderthals and modern non-African humans suggesting admixture between both groups after modern humans left Africa (18)(19). This admixture should have taken place in the contact zone between Neanderthals and the humans leaving Africa: Levant, Caucasus and Europe. If so, the highest frequencies of B006 should appear in these areas and drop off as the populations moved out of that region and admixed with other human groups. However this is not reflected in the global distribution of B006. Although there is a high frequency of the haplotype in the Neanderthal homeland of Western Eurasia and the Indus region (19)(20), America has the highest global value for this haplotype. This suggests a “significant presence of Neanderthal lineages in the Americas” (21), prevalence which can be most parsimoniously explained if the Neanderthal gene flow took place in America. There is a minor “hot-spot” on Western Beringia which may indicate an “Out of America” migration as suggested by some authors (22).

It is argued that American preponderance of B006 haplotype and the loss of other haplotypes (B002, B008 and B005) is due to a major population bottleneck during the peopling of the Americas (23)(18). We propose instead a Post-Hispanic bottleneck that obliterated those haplotypes.

SLC16A11 gene

This gene’s “risk” haplotype is a common risk factor for type 2 diabetes among Native Americans, and is present among them at a ~50% frequency while only ~10% of east Asians carry it. The Neanderthal from Denisova cave carried the mutated gene which is rare among Europeans and Africans, suggesting that it introgressed into modern humans in Asia (24) or, assuming admixture in the region of highest frequency, in America and from there it may have back-migrated to East Asia (22).

APOBEC3G gene

The NE1 allele of APOBEC3G (a gene which may be related to anti-viral immunity) displays a strong cline from America to the rest of the world. It is found in two very divergent haplogroups (25):

• NE1 "aligned with the Neanderthal haplotype" absent in Africa and most Asians and found at mid frequencies in Europeans and Indians ~20% (strikingly similar to Neanderthal B006 distribution). Once again, American Indians present the highest global frequencies (~30%).
• Non-NE1, which aligns with the chimpanzee haplotype and is therefore the ancestral type; it is found in all populations, being highest in Africa (75 - 100%) and Eastern Asia (~75%). In Europe and America its frequency much lower: roughly 33%. This echoes the basal human signature common to all populations.

As with B006 and SLC16A11 gene, the highest global prevalence of NE1 is found among Native Americans, suggesting, again, that the Neanderthal – Modern human introgression occurred in America.

Human leukocyte antigen (HLA) system

HLA are the loci of genes which encode for major histocompatibility complex (MHC) in humans and as such have an important role in the immune system.

Ten Neanderthal HLA class I alleles have been found among humans: A*02, A*26, A*66, B*51:01/08, B*07:02/03/06, C*16:02, C*07:02.

Of these, two are found among Native Americans: The paired alleles A*02 and C*07:02. While their average global frequency is ~2% , the highest global frequency occurs among the Yucpa of Venezuela (26.9%), followed by Navajo, US (13.1%) and Lisu, Yunan, China (10.4%).

The high frequency in America and China is consonant with the high proportion of Neanderthal admixture in those regions. (15). Other allele pairs are found in Asia but not in America, suggesting different populations of Neanderthals as sources of the introgression. The highest global value for HLA-C*07:02 is also found among the Yucpas (71.4%).(26)

The non-Neanderthal Amerindian HLA harbors a great diversity and is markedly different from that of the rest of the world; it clusters separately from all other global populations (especially Asians and, as expected, North American Na-Dene and Inuit)(27)(28).

The High mortality during the European-Amerindian contact period in the 1500s shows that Amerindians carried many unique HLA clades, different to Eurasian lineages and ill-equipped to cope with Old World disease. These became extinct. Current clades are those that were better adapted, among which are the archaic Neanderthal HLAs.

Amerindian HLA diversity could have been caused by:

1. A very long Amerindian isolation.
2. An autochthonous Amerindian origin.

The first option is not concordant with the theory that present day Amerindians came recently from Siberia through Beringia, however it could mean a long period of isolation in America of the original population that carried those HLA clades: the Neanderthals.

The second option would imply a modified version of the multiregional origin of humans (27)(22), which after admixing in America with more archaic hominids, back-migrated into Eurasia.

Blood groups

Amerindians and Neanderthals also share a very high frequency of O blood group.

Most human populations except Native Americans carry all major ABO blood alleles. Amerindians belong almost exclusively to the O group (85.5% in North America and 90.9% in South America versus. a global average of 69.2%).

There are a large variety of O haplotypes in America, such as the widespread and uniquely Amerindian mutation O1v(G542A) assumed to have emerged in Beringia as a founder effect (29)(30).

The ample distribution of O1v(G542A) could also be explained by admixture with a Neanderthal population carrying the allele, which arose promoted by the selective advantage of conferring resistance against the infectious diseases of the New World (31). On the other hand, the alleged "cradle" of Amerindians, Eastern Asia has the highest global frequency for type B blood allele. America, as expected has the lowest, mostly among in Western Alaska due to recent East Asian admixture.

Earwax (ABC11 gene)

There are two varieties of cerumen (ear wax) among humans: dry and wet. Dry is highly common (96%) in Eastern Asia (China, Mongolia and Korea), and among North American Na-Dene and Inuit (70 - 43%), once again suggesting their recent arrival in America.

The Wet wax, believed to be the ancestral form, predominates in the rest of the world: among Denisovans (8), among Africans and Europeans (100% frequency) and among Amerindians (96%) (32); being lowest among those who received a recent (<6 Kya) trans-Pacific genetic influx of Y hgC3* from East Asia (33).

This gene indicates that the original peopling of America by modern humans occurred before the development of this mutation among East Asian Mongoloid groups. This is also attested by craniological interpretation (34): “Caucasoid” shaped skulls found in America differing from the East Asian cranial morphology and “Americanoid” skulls described for Siberia and Central Asia (33)(35)(7):

Mal'ta genetic sequence

The genome sequenced from a 24 Kya H. sapiens (named MA-1) from Mal'ta in south-central Siberia suggests that between 14 to 38% of Native American autosomal ancestry originated through a gene flow from this population.

MA-1 is closer to contemporary Native Americans than to Northeast Asians suggesting that those groups may have originated in secondary wave(s) of immigrants from East Asia (7), or that back-migrations from America dispersed other lineages in Central and Western Eurasia (22).

MA-1 has distinct differences that set it apart from Native Americans: it lacks shoveled incisors (supporting a possible introgression of this gene in America), and its nuclear and mtDNA haplogroups (hg) are different; its:

• Y chromosome is hg R; frequent in Western Eurasia and India but much younger than the hg Q present at very high frequencies all across America and in a limited region in Northern Central Siberia.
• mtDNA is hg U, which is not found in America or East and South Asia and is very frequent in Western Eurasia, India and North Africa.

Nevertheless, Ma-1’s estimated shared drift statistic, (f3), places Amerindians closest to Northern Europeans and Northern - Central and Western Siberians, and furthest apart from Eastern Siberians and Asians. Possibly indicating a common Neanderthal background, which could explain the European signature found in pre-Hispanic Amerindians (i.e. Kennewick man).

Diego blood group

The Diego blood group system is absent among Africans, Australian aborigines, almost all Asians, and all Europeans. It is essentially a Mongolian feature although it is not present in all populations:

• East Asians: its frequencies range from 2% to 8%
• Amerindians: highly variable values between 0% and 50% (36)

It is absent or found at very low frequencies among Na-Dene and Inuit in northern North America and among the Waica, Warrau-Guayo and Yaruro of South America (37). Among the Andean Native Americans it has a North-South decreasing cline.

The distribution pattern suggests that the original inhabitants belonged to the first wave to people the New World, which lacked the Diego allele and which were later overrun by a wave of Diego-positive groups (38). These first comers could be of Eurasian origin (Neanderthals) and the other wave(s) including those in Northern North America had a strong East Asian component.

Microsatellite Locus D9S1120

There is a unique allele (also known as GATA81C04 or GATA11E11) not found anywhere else in the world which is present in all American populations (and some Western Beringian groups - perhaps due to back-migration out of America) at an average frequency of 31.7%, which is not found anywhere else in the world. (39)

This is probably an ancient Neanderthal signature shared by admixture with later arrivals in America. Its high variability from 10% among the Seri to 97.1% among the Surui possibly reflect genetic drift.

Eye pigmentation
Blue eye gene (the derived G allele of SNP rs12913832) is found at ratios of 15 to 29% in South America, although it does not express blue eyes in Amerindians. It is virtually absent in North America and Eastern Asia. It reappears in Central Asia and Europe (40). It is believed to be a recent Neolithic mutation c. 6 - 10 Kya, originated in the north of the Black Sea (41).

However, based on its extended global distribution pattern we differ and propose instead an archaic origin for this gene. Eye pigmentation and skin pigmentation are closely related. Pale skin pigmentation especially for groups inhabiting high latitudes was selected for to allow sunlight absorption necessary for vitamin D synthesis. It is likely a Neanderthal trait since it highest frequencies coincide with the areas where other Neanderthal genes are most frequent. Nevertheless it has not been reported in their genome sequences.

Closely related Oculocutaneous albinism II (OCA2) gene shows the opposite trend, with high frequencies of the derived His615Arg allele in Eastern Asia (49-63%) and nil presence in the rest of the world.

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© 09.January.2014. Austin V. Whittall

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