April 17, 2013

Y-chromosomes of Native South Americans (Roewer et al. 2013)

It would be useful to sequence these South American C3* Y-chromosomes to see how they are related to the C3b-P39 found in some native North Americans as well as other unresolved C3* from Asia. It would also be worthwhile to look at autosomal data from these populations, to see if they are wholly descended from First Americans, or have evidence of more recent gene flow from East Asia.

PLoS Genet 9(4): e1003460. doi:10.1371/journal.pgen.1003460

Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans

Lutz Roewer et al.

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.

Link

13 comments:

Ezr said...

And so the plot thickens. Anyway, their peculiar usage of the term "language class" (?) using classifications that most linguists reject obviously caused unnecessary confusion and led to some odd conclusions on the linguistic front.

Also, I'd like to know how they can so confidently dismiss the possibility that South America simply preserved ancient diversity that has been lost further north. This might be just the beginning and, as more C is found elsewhere, the estimated time of arrival could change.

RayBanks said...

Theoretically there could be a joint new C3b mother group for both Amerindian C groups, but I do not think so.

Maria Geppart is the co-author here, and she previously proposed this late C3* introduction. Both authors ignore in this article the raw C3* data from another study which had divergent Colombian C3* haplotypes from the Andean C3* men.

I have gathered the previous info on one page at
https://sites.google.com/site/haplogroupcproject/c3
Note the significant STR difference between C3b and C3* Amerindians, my project Central * East Asia C3* men are also divergent from both these haplotypes.

Ray Banks, C Project

terryt said...

I would have thought it was obvious that Y-DNA could travel far beyond the distribution of any language it had been originally associated with. Surely it is entirely possible that the South America Y-DNA C is the same haplogroup that appears to have brought the Na-Dene group of languages into North America.

"It would be useful to sequence these South American C3* Y-chromosomes to see how they are related to the C3b-P39 found in some native North Americans"

I would expect them to be the same, or recently derived from it.

DocG said...

"how they can so confidently dismiss the possibility that South America simply preserved ancient diversity that has been lost further north."

Excellent point! As an Ethnomusicologist, I've studied the distribution patterns of world musical styles for a great many years, and can say with some confidence that the distribution of c3* as reported here correlates quite well with the distribution of both singing style and instruments. There are very significant differences in this respect between North and South America, with Central America serving as a kind of intermediate zone.

My own thoughts on the significance of the musical discrepancy are closely aligned with a theory presented back in 2003 by Stephen Oppenheimer, whose analysis makes a great deal of sense, musically, linguistically and now, apparently, genetically. For details see his book "The Real Eve," and also Chapter 15 of my own book, Sounding the Depths, which draws heavily on Oppenheimer's ideas: http://soundingthedepths.blogspot.com/2011/03/chapter-fifteen-upcoast-downcoast-from.html

DocG said...

Correction. Sorry, I wrote my previous comment before studying the paper carefully enough. The distribution of the musical style I have in mind is far wider in S. America than the distribution of c3*, as found by these investigators, which is very localized. So, from my point of view, it might not be as meaningful as I thought.

On the other hand, if the geneticists are reading here, and are interested, they can contact me, and I'll be happy to supply them with the names of some groups not on their list that they might want to look into. My email is victorag@verizon.net

Jim said...

"Surely it is entirely possible that the South America Y-DNA C is the same haplogroup that appears to have brought the Na-Dene group of languages into North America"

There is a huge distance between even the southernmeost Athapaskan groups and south America, and this southern reach is recent. What historical path of migration could explain finding the same haplotype in such widely separated places?

terryt said...

It has just suddenly occurred to me that I have often wondered whether pottery had been introduced from the Atlantic or the Pacific. American pottery was much too ancient to have been brought in by Polynesians, and so I accepted the possibility that it was an indigenous development in America. But perhaps pottery was introduced to America from Japan or China. By Y-DNA C3. If that is the case we are able to date C3's arrival fairly accurately.

Ezr said...

@terryt

Yes, IIRC there are a couple of studies suggesting an eerie similarity between late Jomon pottery from Japan and contemporary pottery from the Ecuadorian coast (sorry, no refs, will have to search for those again), in fact fairly close to the region that is the focus of this paper!

Also, C3* is particularly common among the Ainu.

Suddenly, it all starts to fit together... :) . Let's see how things play out.

Ezr said...

My apologies, I'll have to post again this time just for clarity:
I just checked the paper again in more detail and it does mention the connections between Jomon and the Valdivia Culture, but I think there is more to it - I probably overlooked it because I was expecting something else; I think there were even earlier cultures in the region that have been connected to Transpacific contact with East Asia, will try to find the refs.

Anyway, we'll have to wait for further genetic data on Ainu C3*. But in light of this and the earlier data on the B mtDNA haplogroup, things are starting to get really, really interesting.

Ebizur said...

terryt wrote,

"It has just suddenly occurred to me that I have often wondered whether pottery had been introduced from the Atlantic or the Pacific. American pottery was much too ancient to have been brought in by Polynesians, and so I accepted the possibility that it was an indigenous development in America. But perhaps pottery was introduced to America from Japan or China. By Y-DNA C3."

No sample of any American population has exhibited Y-DNA that belongs to D-M174 or O-M175. Therefore, a hypothesis of an arrival to northwestern South America of C3-M217(xC3b-P39) from China or Japan at some time within the past 6,000 years is only plausible under at least one of the following assumptions:

(1) C3-M217(xC3b-P39) was introduced to northwestern South America by a lone individual or a very small group of individuals (shipwrecked fishermen?), of whom only one individual (or a few patrilineally closely related individuals) managed to leave patrilineal descendants in the New World.

(2) C3-M217(xC3b-P39) was introduced to northwestern South America at a time when some population(s) in East Asia contained only C3-M217 Y-DNA (or some combination of C3-M217 and Q-M242 Y-DNA), prior to admixture with other populations whose males bore Y-chromosomes derived from N-M231, O-M175, D-M174, or C1-M8.

It is implausible that the ancestor of South American representatives of C3-M217 has arrived in the New World as part of planned trans-Pacific intercontinental interactions undertaken by people identical to any modern East Asians. One would have to believe in some extreme sort of selection acting on Y-DNA in order to even consider such a hypothesis.

I know you have not made any such radical claim. I am only making this post as a precautionary measure.

terryt said...

"But in light of this and the earlier data on the B mtDNA haplogroup, things are starting to get really, really interesting".

I did consider for a while that mt-DNA B had come in with Y-DNA C3 but I decided B looks too ancient to fit that scenario. In favour of the idea, though, is that B2 (or B4b2 as it should perhaps be called) has no close relations along any Beringia route, so is unlikely to have entered America via that route. In fact some clade of B4b1, B2's closest relation, reached the Admiralty Islands, presumably as part of the Austronesian expansion. It was also accepted for many years that aspects of the early Austronesian culture and technology arrived direct from Japan rather than via the mainland. I'm not sure where that idea stands today, however the main Taiwanese Austronesian haplogroup, B4a, is firmly rooted in SE Asia and Southern China.

"There is a huge distance between even the southernmeost Athapaskan groups and south America, and this southern reach is recent. What historical path of migration could explain finding the same haplotype in such widely separated places?"

A coastal migration followed by irregular movement inland? Perhaps the Athapaskan arrival in America is not particularly ancient. Are they known as pottery users?

G Horvat said...

If Jomon pottery makers were female, then, at best, NRY C3* would have accompanied the pottery-makers and, so, one could not draw conclusions from the Y chromosomes alone. A type of mtDNA sequence which has: 1) been postulated, in the past, as having been brought to the New World separately, 2) which is rare in North America and 3) which was determined to be quite common in an Ecuadorian sample is D4h3a. Of course, the earliest known incidence of this sequence precedes early and middle Jomon as it was present in On Your Knees Cave. The Tlingit, who inhabited the region surrounding OYK cave, is one North American population which was determined to have C3* Y chromosomes.

terryt said...

"No sample of any American population has exhibited Y-DNA that belongs to D-M174 or O-M175".

To be honest Ebizur I hadn't given the slightest thought as to where in East Asia American pottery may have spread from. But you raise an interesting point which deserves to be followed.

"C3-M217(xC3b-P39) was introduced to northwestern South America at a time when some population(s) in East Asia contained only C3-M217 Y-DNA (or some combination of C3-M217 and Q-M242 Y-DNA), prior to admixture with other populations whose males bore Y-chromosomes derived from N-M231, O-M175, D-M174, or C1-M8"

On studying the problem a little I prefer that explanation. Y-DNA O in Japan is almost certaily associated with Yayoi and so is after any relevant connection between pottery/Y-DNAC. But D remains a problem, unless Japan is not the direct source. I printed off some information you supplied some years ago where you have Y-DNA C3 making up a substantial proportion of Nivkh as well as the people of Kamchatka. A migration into America from either region would include Y-DNA Q which would largely blend into what we see as the haplogroup landscape.

"there are a couple of studies suggesting an eerie similarity between late Jomon pottery from Japan and contemporary pottery from the Ecuadorian coast"

And both perhaps with some other region? Anyone know anything about ancient Kamchatka pottery? Most should find this link interesting:

http://www.cemca.org.mx/UserFiles/files/final%20edit%20%20kamchatka_article_english_final[1].pdf