Peoples genes and their languages may not share a common origin. As an example of this we have the Portuguese language which is spoken by the Portuguese (with European mtDNA) and Amazonian Brazilians (with Amerindian mtDNA) or Angolans (with African mtDNA) or even some former Macao inhabitants (with Chinese mtDNA).
Of course the changes brought on by the European sixteenth century's discovery and conquest of the World was quite unprecedented due to its global scale (the conquerors were mostly men -hence the lack of European mtDNA among the current local ex-colonials- but, they did impose their homeland's language on the locals).
There were similar (scaled down) migrations in historic and prehistoric times, so it is quite complicated to tag genes to language. However L. Luca Cavalli-Sforza has been doing this since the mid 1960s. Today's paper is inspired by his work, while I was re-reading a very old article in a 1989 Scientific American issue dealing with mtDNA and languages.
Languages of the World
There are several thousand languages dispersed across the globe, some are mega-languages spoken by hundreds of millions (Mandarin Chinese, English, Spanish, Portuguese) others are on the verge of extinction. And all originated from those spoken by the first Modern humans to appear in Africa some 150 kya.
The map below shows a rough grouping of the languages spoken around the world.
As we can see, they can be grouped into four large clusters (based on similarities and shared origins):
- Eurasiatic. This is a "superfamily" spanning most of Asia and Europe.
- African, which combines the African Languages.
- Isolated languages, some “isolated languages” such as Dravidian in India and the Kartvelian languages in the Southern Caucasus.
- Rest of the World, whith the different languages spoken in Southeast Asia, Australia, New Guinea and the Americas
You know that an Early peopling of America is my pet subject, so the large diversity of languages found in America and their potential links (or lack of them) with the purported Asian homeland of American Natives is something to look into.
If American Natives originated in Eastern Asia or Siberia, you would expect them to have languages similar or closely related to those currently found in those parts of Asia.
Well, it is not excactly like that: some North American natives speak languages that are close to Asian languages, but the majority of the Amerindians, from all over America, do not.
Native American languages form three distinct groups:
- Eskimo Aleut. Spoken in the northernmost part of America (around the Arctic and in Western Alaska). These are, according to theory, the most recent arrivals in America.
- Na-Dene speakers. These are only found in some areas of North America (whose people speak Na-Dene). Their languages form part of a Super-family known as "Dene-Caucasian", which spans Asia. In our map above, it is shown in yellow.
- Amerindian, shown in the map in turquoise color, spanning most of the Americas.
The Na-Dene language belongs to the Dene-Caucasian superfamily which includes those speaking Sino-Tibetan (the Chinese and Tibetans), Yeniseian languages (a small strip along Yenisei River in Central Siberia) and some other isolated groups:
- The Basques in Spain and France. Which are the westernmost members of the group. They are particular people in many ways. Language is one of them.
- The Caucasians in the Caucasus area. Both Basque and Caucasian are closer to each other than to the other Dene-Caucasian languages. By the way there are other non Dene-Caucasian languages in the Caucasus, such as Kartvelian. Clearly this area was an area of admixture and communication (Middle East and South Asia with the Russian - Ucranian plains to the north)
- Burushaski, spoken in Northern Pakistan. It is an isolate language is close to one spoken by the Yeniseian people. Both of which are closer to each other than to the Sino-Tibetan and Na-Dene langauges (both of which are also closely related to each other).
The fact that these languages are "scattered" across a wide swath of Europe, Asia and America means that they probably occupied a vast area and that later (please see the map above), people speaking Uralic, Indo-European, Chukchi - Kamchatkans, Altaic and Eskimo-Aleut, moved into their current areas displacing or replacing the original or ancestral Dene-Caucasian speakers.
Since they occupy most of the Continent, especially the southern cul-de-sac, they were very likely the first people into America, predating both Na-Dene speakers and Eskimo Aleuts.
The three clear-cut language divisions in America led Greenberg  to postulate a three wave migration theory to explain the peopling of Americas: first came the South and North American Amerindians. They were followed by the Na-Dene pople (Navajo, Apache, Athabaskans) and finally the Eskimo-Aleuts.
There is some genetic corroboration of this theory since Eskimos are mostly Q1a6 (M323*- NWT01) Y chromosome haplogroup (Y hg) which is not found among Amerindians, while C3b Y hg is frequent among the Na-Dene but infrequent among the other Amerindians.
On the matrilineal side: D3 mtDNA is found among Eskimos while D2a is frequent among Na-Dene, Tlingit and Aleutians. Na-Dene, Aleuts and Eskimos are also A2a. None of those haplogroups are found among the other native people.
There are also notable differences between the three group's HLA (the loci of genes which encode for major histocompatibility complex in humans and as such have an important role in the immune system).
In a previous post (An Early Peopling of America) I pointed out that "...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)." (Inuit = Eskimo).
The variety of Amerindian languages which are quite unique and, unrelated to others, plus those distinct markers indicates that the first humans to enter America were not related to the Dene-Caucasians or those people currently inhabiting Western Siberia or Asia.
Could these languages be linked to a hypothetical archaic human language or even a Neanerthal language?
Let us go back to the Dene-Caucasian languages, which seem to predate the other ones in Asia.
The isolate Buruchakski language spoken in Northern Pakistan's mountain areas is quite unlike other languages. It has picked up Indo European traits due to its long co-existence in close contact with speakers of those languages, but it retains its unique features.
It is closer to the Yeniseian speakers than to the Sino-Tibetans, suggesting that there is an East - West split among the Dena-Caucasian speakers (Sino-Tibetans and Na-Dene in the East, and Basques, Caucasians, Yeniseians and Buruchakskis in the West).
Furthermore, the Buruchakski language is anciente; according to Bengston and Blazek:  "There is evidence that early Indo-Aryan was influenced by Bur (or perhaps a wider ranging Burushic family) as its speakers entered the Indian subcontinent by way of the Hindukush and Pamir regions...", they also suggest that there was a "remote ancestor (Borean) common to the ancestor of Indo-European (Nostratic or Euroasiatic) and the ancestor of Buruchakski (Dene Caucasian)".
It is clear that Buruchakski entered Northern Pakistan from the North, maybe from central Siberia, but since this route was blocked by Ice Age Glaciers during the period of Neanderthal - Modern Human contact, we can assume that they had not yet reached their current homeland, and that their ancestors lived further north, in the area of Yenisei and Altai.
Ancient Humans or even Neanderthal language?
The area covered by the Dene-Caucasian language reminds me of the Neanderthal "homeland" (see my post on this here), where I posted the map that I reproduce below (with some changes regarding Neanderthal's later dispersion):
Neanderthals occupied a large swath of Eurasia before modern humans left Africa. The "invading" Homo sapiens (blue arrows -map above) must have put the Neanderthal on the move, or perhaps they too were already moving Norteast (red dotted arrows) prompted by the same global change that prodded Modern humans out of Africa.
Could Amerindian languages or "Dene Caucasian" languages be related by this hypothetic ancient remote ancestor Borean, or an even older language?, a Neanderthal language.
Let's suppose that Neanderthals spoke a language which we can call "Nenderspeak". It moved with them as they pushed into Siberia and as they shrunk into the corners and inhospitable areas of Europe as a consequence of modern human's onslaught into that continent. This would be similar to the Gaelic speaking Celts of Britain and France, who retreated into the "peninsulas" of Normandy, Wales, Cornwall and Scotland when the Anglo-Saxons invaded their territories.
Modern humans spoke a different language (or languages), which originated the other Euro-Asiatic languages: Altaic and Uralic which occupied most of Northern, Central and Eastern Siberia as well as Eastern and Northern Scandinavia. While Indo-European would spread out from India across the rest of Southwestern Eurasia.
But who spoke "Borean"? could ther have been more than one wave of humans? some speaking "Borean", the others speaking the ancestor of the other Eurasian languages?
Y haplogroup O and C roughly covers the area of Borean (Dene-Caucasian) speakers, while Y Hg J, G, I, L, H, R and N cover the rest of Eurasia. On the mtDNA side, Eurasians are mostly U, H and J mtDNA all descended from the N line, while the Boreans are M line (D, C).
This indicates that there were two groups of humans with their set of languages, coinciding with the N, M mtDNA haplogroup split after they left Africa. Maybe the M group spread first and was later replaced (in the West) by N lineages (this explains the Caucasus and Basque pockets of Borean speakers).
Meanwhile, as I mentioned in my previous post (An Early Peopling of America) here, the Neanderthals "moved east from Central Asia expanding into China during MIS 3 times -29 to 58 Kya. , as attested by a high presence of Neanderthal ancestry in Eastern Asians ...". The map above shows this migration with the solid red arrows.
Did their hypothetic "Neanderspeak" language move with them into China and Tibet, and up along the Yenisei River valley (red oval in map)?
More introgression ocurred when modern (M mtDNA) Humans advancing behind the Neanderthals entered Siberia and, crossing India and Southern Asia, entered China.
Their Borean language evolved in each of these locations, becoming Dene-Caucasian. Northeast Asia was vast and empty except for the few Neanderthal that lived there, hunting the big prey.
Only much later (5-10 kya) would the ancestors of the Burushics cross the Himalayan passes and occupy Pakistan, only to be pushed back as the Indoeuropean people spread out from India across Europe, displacing and replacing the Dene-Caucasian language speakers.
This explains the distribution of Asian and European languages quite well. But what about America?
American Languages another view
Following their game, part of the Neanderthals entered America and spread out across both North and South America. "Neanderspeak" evolved into proto-Amerindian languages.
They were followed by the ancestors of the Amerindians who did not speak "Dene-Caucasian", which based on my assumptions oulined above, hints at a N mtDNA linage and a Y hg closer to Europe than to Asia. And this is exactly what was found in the genome sequenced from a 24 Kya Homo sapiens (named MA-1) from Mal'ta in south-central Siberia:
- Between 14 to 38% of Native American autosomal ancestry originated through a gene flow from this population. (Ancestral to Amerindians).
- MA-1 is closer to contemporary Native Americans than to Northeast Asians. (The late arrivals speaking Altaic or Chuckchi - Kamchatkan)
- MA-1 belongs to Y chromosome hg R; frequent in Western Eurasia and India but rare in Eastern Asia. (So their language was not "Dene-Caucasian")
- Its mtDNA is hg U, which is not found in America, East and South Asia but is very frequent in Western Eurasia, India and North Africa. (Supports the language theory).
Further proof that ratifies the above. Today, before posting what I had written over the last few days, I read Chapter 10 of Merritt Ruhlen's On the Origin of Languages: Studies in Linguistic Taxonomy, Stanford University Press, 1994. Which I quote below:
"Finally, I will present evidence connecting the Amerind family with the Eurasiatic family. It should be pointed out that additional connections between Amerind and Eurasiatic are given in Chapter 14 herein. The etymologies given there, however, connect both Amerind and Eurasiatic with other other language families."
Amerindians have high frequency of Y hg Q which is only found outside of America among some central Asian groups (i.e. the descendants of the Mal'ta people).
Amerindian mt DNa is more complex, but South America shows a mix of both M and N origins (high frequencies of hg D and C, one evolving from M, the other from N). In North America A and B are prevalent (+75%) among the Na-Dene and Eskimos (the latest arrivals in America) and also at +50% among other Amerindians. This is surprising since both are N lineage and one would expect them to belong to an M derived Haplogroup.
Since B is also found in China (20-40%), and A (10-20%) also, and as we have already mentioned close ties between Na-Dene and Sino-Tibetan languages, it may indicate that the Na-Dene people originated in that area and had predominant N lineage mtDNA yet spoke a "M mtDNA" language, walked across an empty Western Asia into America. The last inmigrants were the Eskimos; then the Altaic and Chukchi - Kamchatkans occupied Northeastern Asia, leaving the current distribution pattern.
Now always bear in mind that the millions of natives that died between 1492 and 1600, due to smallpox, flu, war, and other diseases took their own mtDNA and Y hg lineages with them. We see a picture of what remained after those that survived re-peopled the continent. So maybe the prevalence of A and B mtDNA in the North and D & C in the South is due to this selective pressure, of adaptation to European disruption.
As proof of the above: in a previous post I mentioned the discovery of mtDNA haplogroup M in Canada, which is now compeltely absent from the New World.
Amerindian language diversity
Why are there so many languages in America. Why did they differ so much in the 15-30 ky that according to orthodoxy is the time that they have been in America while the rest of the world in more time than that evolved less languages?
They did so for the same reason that Papuan languages (another hot-spot of diversity) diversified and differ from those spoken in South East Asia or Australia (although the Papuans did so in more time: 50 ky): 
- Time. We are talking about, in my opinion of +40 to 50 ky, plenty of time for languages to diversify and change.
- Terrain. Promotes higher language density (Mountains: Papua New Guinea, Caucasus, the Andes and Rockies in America) and so does the other geographic barriers: swamps and jungles, wide rivers, deserts, vast prairies, 4 km (13,000 ft) high plateaus...
- Tribal systems. The splintering of groups into tribal entities with unique identities, living isolated from each other promotes linguistic diversification. This contrasts with nation states that impose their language on all their subjects, thus promoting uniformity.
But what happened to the Neanderthals?
They "mixed" with modern humans, those that were the Paleoindians that were the ancestors of the Amerindian speakers. Genetic proof of introgression exists (see my paper An Early Peopling of America on this subject).
Their language "Neanderspeak" influenced the languages spoken by the invaders, shaping Amerindian languages.
However there is no exclusively American mtDNA among Amerindians a mtDNA that may have a Neanderthal origin.
The same can be said about Y haplogroups: the Lack of Neanderthal Y hg may mean extermination of Neanderthal males and mating with Neanderthal females done by Modern Humans belonging to Y hg Q.
Since Neanderthal mtDNA is absent among extant Amerindians maybe the female issue of human-Neanderthal couples were infertile and⁄or that the great bottleneck caused by disease and war during the conquest (post 1492 AD) led to the demise of ancient Neanderthal mtDNA lineages.
But all this is hypothetical. We don't know what language Neanderthals spoke (We do know that they did speak  and it is possible that the common ancestor of both Neanderthals and modern humans may have been capable of speech too! ).
There is also no solid evidence of them ever entering America or even living in Norteastern Asia, Western Siberia or Beringia.
But who knows what further genetic studies may unearth?
 L. Luca Cavalli-Sforza & Marcus W. Feldman, (2003). The application of molecular genetic approaches to the study of human evolution. Nature Genetics 33, 266 - 275 (2003) doi:10.1038/ng1113
 Greenberg JH, Turner CG, Zegura SL., (1986). The settlement of the Americas: a comparison of the linguistic, dental and genetic evidence. Curr Anthropol 1986; 27:477-498
 L. Luca Cavalli-Sforza, P. Menozzi, A. Piazza, (1994). The History and Geography of Human Genes. Princeton University Press, Princeton
 John D. Bengtson and Václav Blazek, On the Burushaski–Indo-European hypothesis by I. Casule. Masaryk University
 Mishra S., Chauhan N., Singhvi A., (2013). Continuity of Microblade Technology in the Indian Subcontinent Since 45 ka: Implications for the Dispersal of Modern Humans. 01 Jul 2013. doi: 10.1371/journal.pone.0069280
 Wall J., et al., (2013). Higher levels of neanderthal ancestry in East Asians than in Europeans. Genetics. 2013 May; 194(1):199-209. doi: 10.1534/genetics.112.148213
 Foley, William A., (1986). The Papuan languages of New Guinea Cambridge: Cambridge University Press.
 D’Anastasio R, Wroe S, Tuniz C, Mancini L, Cesana DT, et al. (2013) Micro-Biomechanics of the Kebara 2 Hyoid and Its Implications for Speech in Neanderthals. PLoS ONE 8(12): e82261. doi:10.1371/journal.pone.0082261
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