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Wednesday, January 3, 2018

A genome from the first founding population of Native Americans (Moreno-Mayar et al. 2018)


Over at Nature at this LINK. By the way, when did Nature start adding those "Life Sciences Reporting Summaries" to its papers? I remember having a chat with Broad MIT/Harvard back in May about adding something like this to ancient DNA papers, especially in regards to data exclusions, right after my blog entry about the somewhat suspiciously missing Yamnaya males in Mathieson et al. 2017 (see here), and suddenly, here it is. Eh, probably a crazy coincidence, but a great move in any case. Below is the Moreno-Mayar et al. abstract and an Admixture graph from the paper:

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved [1,2,3,4,5]. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka)6. Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans [1,7,8]. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20 ka, with Ancient Beringians branching off around 22–18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model [9]. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6 ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos [1], Inuits or Kets [10], and that Native American gene flow into Inuits was through northern and not southern Native American groups1. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.


Moreno-Mayar et al., Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans, Nature, Published online: 03 January 2018, doi:10.1038/nature25173

75 comments:

Sofia Aurora said...

Since this is the first post of the new year HAPPY NEW YEAR folks!
May 2018 offer you all health and joy!

Anonymous said...

@Davidski

Could you do:

Mbuti GoyetQ2-116 Mixe Suruii?

jv said...

Interesting! Thank you! I find Native American artifacts behind our house and have a collection.The Archaic Indians found chert nodules on this hill and heat treated the soft chert in Earth ovens to improve it’s quality. ( so far, Ive found 3 Earth ovens)I’ve always been fascinated with these true Early Americans and especially after moving to this hill.

Ryan said...

Any idea when you’ll be able to get your hands on the DNA? It would be interesting to see where this group stands in terms of its affinities to Denisovans and to Oceanians, since those structures in indigenous Americans are still unexplained.

I wonder if East Asian link between Kets and Athabaskans would be a link between Sino-Tibetan and Dene Yenesian.

And who bets us Indo Europeans would end up on the Koryak branch of ANE?

That Saqqaq Greenland link seems to contradict previous findings though.

Unknown said...

Good evening everyone. First post. No axes to grind.

At the risk of returning to topic, if we can now be confident that Native Americans split from Beringians (as represented by USR1) between 22ka –18ka, then this becomes a secure date range for the first settlement of north America south of the ice. And it does fit well with the current dating for Meadowcroft, Monte Verde and other pre or proto-Clovis sites.

However, this same period was the peak of the LGM and has always been excluded for first settlement on the basis that the southern Alaskan and Canadian coasts were fully glaciated and impassable. Which seems to imply a direct sea crossing from the Aleutian Islands to Vancouver Island or even further south. A 1000 mile journey in a small boat through iceberg infested seas is impressive today - but at 20ka? Surely not?

So I strongly suspect parts of the picture are still missing (or wrong). Any ideas anyone?

Davidski said...

@epoch

I can't run any stats at the moment. Not for another week or so.

Lee said...

@watkins M

A similar idea was posulated by Dr. Bruce Bradley and Dennis Stanford but Across the atlantic Ice. They do a fairly good description of how such a journey could take place.

You also need to account for lower sea levels at the peak of the Ice age of nearly 400 feet. Islands along the coast and coast areas not present today were likely present.

Chasing seals and whales down the coast would have been possible. They could have camped out overnight on ice or islands. Inuit can do it today with fairly primitive crafts. North pacific currents may have been helpful to push the boats to the south as well.


CleverPrimate said...

I will be interested to see how these genomes compare with that of Kenniwick man.

Ric Hern said...

I wonder how trees populated Canada so thoroughly after the Ice melted ? Were their seeds frozen for hundreds of thousands of years ? Did animals spread their seeds from the South or did they spread from Beringia at some time before waterlevels made it impossible ?

Lee said...

@epoch2013


result: Mbuti GoyetQ116-1 Mixe Surui 0.1546 0.126198 1.225 9 7 806

Really very few SNP's in common--probably due to low quality of GoyetQ116-1

Samuel Andrews said...

"8,000 YEARS AGO, 17 WOMEN REPRODUCED FOR EVERY ONE MAN"

https://psmag.com/environment/17-to-1-reproductive-success#.uwa9wqm4n

This is an easy to make miss interpretation of mtDNA/Y DNA data. Human Y DNA is dominated by "young" founder effects which date to the Neolithic or *later* (like R1b L151 or R1a Z282) while there are 100s even 1,000s of mHGs in most populations which date to the same period.

This doesn't mean 17 women reproduced for every man. Most men and most women had kids. What it means is for whatever reasons, probably patriarchal reasons, certain Y DNA lineages had more sons. This definitly doesn't mean the invention of farming created these popular Y DNA haplogroups.

Davidski said...

@Lee Albee

If you're only getting 806 SNPs in that stat then there's a serious problem with your dataset.

Lee said...

@Davidski

I merged Reich and Willserlev lab samples via Plink. Some of the data did not merge easily and had to finagle it a bit, I think due to different chip sets used in various samples.

I had to use Genotype Harmonizer to get some of these sets to merge. Used the human panel diversity panel from Reich lab(Human Origins Panel from Lazaridis et al. Nature 2016) as the reference population following conversion into Plink format.

Do you have a alternative method you use to merge files?

Lee

Unknown said...

@Davidski Oh David, you mentioned something about Yamnaya samples in the study, though I couldn't find them, do you know where they are?

Thanks bro.

Davidski said...

@epoch

Alright here you go, based on ~400K SNPs.

Mbuti GoyetQ116-1 Mixe Surui 0.0072 1.724 412814

@Lee Albee

I just use PLINK to merge everything, and a Python script to make sure that the positions are all correct.

If you don't want to fiddle around like that, then maybe try the binary designed for merging eigenstrat datasets, I think called mergeit, or something similar.

Davidski said...

@Shahanshah of Persia

There are no Yamnaya samples in this study. You need to read more carefully what I wrote.

Anonymous said...

@davidski

Thanks. No discernible link between the Goyet admixture and the mystery admixture in Indians in Tianyuan. Would be a surprise though, because I can't believe the authors of that paper wouldn't have tried that themselves.

@Lee Albee

Thanks for the effort nevertheless.

Unknown said...

@Davidski Thanks, mate. Any update on the Rakhigarhi paper? Someone alerted me to the fact that there will be TWO papers published, one Harvard/Nature one, and the other by the Indian researchers. If this is true, could there be a chance that the Indian researchers might purposely misreport the data? Thanks Dave.

Lee said...

@ Davidski

Yep put it back together with mergeit--sans most of the willserlev data which are the ones that gave me issue

Got similar results as yourself when I put it back together
result: Mbuti GoyetQ116-1 Mix Surui 0.0067 0.004040 1.651 16922 16697 427310

so it looks like the harmonizer software was getting rid of alot of snps for some reason.

not that 400K or 806 snps showed a major difference in the interpretation of the results--but more snps is more robust.

Thanks for pointing out the issue with the files. I am going to have to redo some analysis and try and remerge the willserlev data into the file.

Lee

Samuel Andrews said...

Off topic, but I think I came to a realization, due to studying mtDNA, on the topic of whether race is real or not. I think David articulated this in another thread. Before explaining my reasoning here's my conclusion; the more distantly in the past a population lived the less likely it can genetically fit very well into a modern racial-continental group but this doesn't delegitimize the idea of race.

What I see in mtDNA is modern populations within huge regions share lots and lots of common ancestry in the last 10,000, 5,000 years, and often much more recently. Russian and Irish mtDNA by most measurements is essentially identical. There aren't many regional, ethnic-specific mHGs.

What this means is humans don't stay genetically isolated for very long. They move around a lot. Genetic continuation won't last for 1,000s and 1,000s of years. New groups "constantly" (once every 20 generations maybe) move in and mix. Modern races aren't similar because they decend from a single founding population who remained isolated for a gazzilion years, they're similar because they decend from the same multiple founding populations who migrated into the same region and mixed with each other over the course of thousends of years. The high genetic similarity between Finns & Irish isn't due to shared decent from a single ancient lineage it is due to having lots of recent common ancestry from the same multiple ancient lineages.

This is also why really ancient populations can't be categorized into modern races. The more ancient the population the more likely it is just one fraction of what makes up one or multiple modern racial groups. ANE is a perfect example. It's closest relatives belong to different "racial groups." ANE makes up an important piece of what defines Ameridians & South Asians & Europeans & more.

Because, ANE or EEF or whatever, can't be categorized into a racial category does that mean race doesn't exist? No. We just have to change our definition of race. It doesn't refer to an ancient pure lineage, it refers to a handful of modern genetic clusters which include huge proportions of humanity and descend from multiple ancient genetic clusters.

I don't use the term race. It is not because I think it is immoral but because it is just a layman's term and not meant for genetic(s). Anthropologist in the past did have a simplistic view of race. This simplistic view isn't due to racism even though many were racist. It was just due to ignorance, a lack of knowledge of human genetics. The same reason so many ethnic groups have origin myths where they claim to decend from a single man.

Unknown said...

@Samuel Andrews There's also the fact that all of us evolved differently from one another, i.e. Caucasoids, Mongoloids, Australoids, and Negroid/Congoid/Capoid.

Grey said...

Watkin M

"However, this same period was the peak of the LGM and has always been excluded for first settlement on the basis that the southern Alaskan and Canadian coasts were fully glaciated and impassable."

That idea has never made any sense to me - don't eskimo live on the edge of glaciers? People can survive as long as they have access to sea food so if the glaciated edges extended 400 miles into the Atlantic/Pacific I'd expect to find people there - along the edge of the glaciation.

It's generally said in relation to maps of the glacial maximum like this

https://i.pinimg.com/originals/0b/00/44/0b0044923e0b8c8b27a7f7412eee3e74.jpg

that humans/archaics were all clustered in southern refugia but personally i think there was probably some much further north as well but only along the sea edge - so maybe some of that got to America that way?

Strandloper said...



please try and stay on the topic of thread for sake of other readers.




thanks

Anonymous said...

I am really interested in that line from East Asia to Athabascan. It only contributed 12%, but could that be the shadow of the Na Dene arrival?

Ric Hern said...

I wonder if a Koryak or Nivkh linguistic connection to the Algic now looks more plausible ?

Mark B. said...

@ Samuel Andrews

I have to disagree with you on the use of the word race (I know it's a touchy topic, but grown-ups should be able to discuss it in it's scientific aspect). Race is not just a anthroplogical term - it's a biological term. If you have two versions of the same interbreeding species of squirrel - one, black in the north, and one grey in the south. you name them races. That's it. The word race gained its usage before DNA analysis existed, and can be used without parsing codons. No zoologist or botanist ever waited to get DNA evidence before they defined races in warblers or sunflowers - if they are fully compatible to interbreed but have a noticeable phenotypic difference, they are races. Essentially, what you (and others of the more anti-racist bent) are asking is that there be NO gene flow. In other words, races can't be races because they are't different species. Which is a definitional non-starter. I just read an article in which a scientist claimed that his genetic analysis proved that there was no such think as 'race' in humans. Which, of course, is non-scientific nonsense. Race is a phenotypic concept that is in the eye of the beholder, but it is perfectly reasonable and rational for all that.

Your positional was staked out in a perfectly reasonable way - I just take issue with it for how others have mis-used it.

MomOfZoha said...

May you have a bright and auspicious 2018, Sofia Aurora.

jv: Are you sure you are not living on an actual mound? :)

In response to this very interesting blog post in general: The complexity exhibited by even this very limited admixture graph is remarkable. And yet, with a couple exceptions (including Yoruba, e.g.), practically all of the nodes in this graph would have been considered "Mongoloid" to pseudo-scientific Coonists. Not to mention that not a single actual Mongolian language is represented, but the variety of divergent branches from ANE and East-Asia that later converge at different points, to be diverged and converged much later again (e.g. especially the structure of the paths leading to the Greenlanders) are remarkable for such a graph including only a small subset of indigenous Siberians.

I would have loved to have seen the statistically most likely positioning of suitable ethnic representatives for more of the given language groups here. If greater isolation/endogamy makes the analysis less "noisy", then at the least some Yukaghir and Even could be included as they are also geographically relevant, living in between the Koryak and the Ket. Ideally, I would also liked to have seen where Tuvan (i.e. Tuvinian), Dolgan, and Nenets would be positioned in the admixture graph as well. David's simultaneous blog post in PolishGenes "On the genomic history of North Eurasia" is coincidentally (probably not a coincidence actually) a good reference for further elaboration in this regards.

I wonder these things:
* Are there any Siberian groups that are "their own" highly divergent branch preceding the split between ANE and East-Asian? There were no such Siberian nor Native American groups so far in the graph so I doubt it, but the question remains.
* Will all of the other indigenous Siberian groups *also* be admixtures of ANE and East-Asian branches, or not? Excluding Yoruba, so far only Mal'ta and Han are the "pure" nodes, corresponding to ANE and East-Asia respectively, which could have been part of the initial modeling assumption for the "seed graph". Koryaks and Kets share a sub-path of an East-Asian admixture branch but are on totally different ANE branches. Whether the answer to this question is "yes" or "no", I *really* wonder the resulting structure when nodes for other indigenous Siberian groups would be added to the graph.
* Given the topology of the graph so far and the admixtures illustrated for both Koryaks and Kets already, I suspect the answer to the previous question is "yes". But, if somehow the answer to the previous would turn out "no", then I wonder further if Nenets would split from just ANE and if Even would split from just East-Asia. Personally, I wonder even more what would be the positioning of Tuvan and Dolgan, and if they would be ANE-East Asia admixtures or not, though I suspect admixture. Then, the question is of course what the whole graph would look like, who would share which parts of which ANE or East-Asia paths with whom.
* Finally, there is the last statement of the abstract: "Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians." Where is this back-migration elaborated upon? It seems it would be significant if it went beyond the more "micro-scopic" dynamics of bilateral Beringian crossings and if it instead resulted in any macroscopic (i.e. "population genetics") effect for any subsequent Siberian groups... This may sound like the stuff of fantasy, even though such micro-scopic dynamics can be sufficient in and of itself to cause macro-scopic change...

jv said...

@ MomOfZoha, no, this is not an Adena Mound, it is a hill beside the river
with limestone bluffs. We had a State Archaeologist out to chat with us. The Archaic Native Americans had a Trail on this side of the West Fork of the White River. Apparently, there were several areas in the county where chert was quarried. The ravine behind the house is one area. However, more recent NA Cultures, like the Adena, hunted here. I found a discarded Adena Point behind our house. However, this point was made from Wyandotte Chert, a very high quality flint type chert from Indiana, not a local chert. I also found a biface behind the house made from a chert found in the Northern part of the state. Seems the chert was traded extensively in this state.

jv said...

Ok, this is completely off topic .... but I’m stoked( as my hipster son would say!) It seems my Father will be able to take a FREE yDNA test! I emailed a Surname Project Administrator today and he will send my Father a test. He is interested in his New England/Early Colonial male ancestor with the same Surname! I’m positively ecstatic about this as we have hit a brick wall with my Great Great Grandfather that died at 27 years old in Baltimore. He may not be from Colonial New England but, I may know more about his origins from this test!

MomOfZoha said...

@jv: That is very interesting -- what an exciting location for your home.

Also congratulations on the free yDNA test for your father. I hope that it will help shed light on your great-great-grandfather.

I recently had my father do a yDNA test with 111 markers, and it turned out unfortunately uninformative: I already knew he was generally Y-haplogroup T1a, but he had zero matches even at the 12 marker level. Neither modern nor ancient. I have him in the T haplogroup project, but still have no updates from the project admins.

I am sure that your father's DNA test will be infinitely more informative, as I expect he will have some interesting matches. And, your surname information will also be useful.

While surnames did not exist in Turkey prior to my great-grandfather's generation, I did discover something about my great-great-grandfather (pure paternal) via the "omniscient" Google years ago. I found mention of him and his village in Sir W. M. Ramsay's 1909 travel diary "The Revolution in Constantinople and Turkey". The Scottish archaeologist Ramsay referred to my great-great grandfather as the "most surly-looking hodja" and to all the villagers in general as "Isaurian mountaineers". Ramsay even attempted to explain the character of the hodja and villagers in terms of adjectives a la Isaurien:
"... or due to the more vigorous character of the Isaurian mountaineers. Dinek Serai lies at the extreme outer edge of the Isaurian hills, and the people of all these hill-villages are more resolute and courageous than the people of the plains."

Anyway, I am tired now as my child is too small to be a hipster just yet. :) But, again, I wish you success in your genealogical endeavors.

Ebizur said...

MomOfZoha wrote, "Koryaks and Kets share a sub-path of an East-Asian admixture branch but are on totally different ANE branches."

This reminds me of a post I made on Anthrogenica last October regarding the haplogroup Q lineages of the Kets and the Koryaks.

A great percentage of extant Kets (and their Samoyedic-speaking neighbors, the Selkups) belong to the Q1b1a3b-B287 clade, which also has a member with reported origin in Astana, Kazakhstan and an estimated TMRCA of approximately 5,000 ybp. Its interclade TMRCA with Q1b1a3a-Y20260, which has been found in an Uzbek and in an individual with reported origin in Nógrád, Hungary, is estimated to be about 8,000 ybp.

In contrast, the predominant Q lineage among Koryaks and other Chukotko-Kamchatkans appears to be a branch of Q1a1-F746/NWT01, although some of them belong to Q1b1a1a-M3 instead, perhaps as a result of mainstream Native American admixture mediated via Yupiks. The Y-DNA of the published Paleo-Eskimo Saqqaq specimen from Greenland also belongs to this clade. The Q1a1a-M120 subclade is widely spread as a minority haplogroup among Sino-Tibetans.

The Ket (and Selkup, Kazakhstani, Uzbek, Hungarian, etc.) Q1b1a3-L330 clade is significantly more closely related to the mainstream Native American (and marginally also Germanic) Q1b1a1-CTS11969/M930 and Q1b1a2-CTS1780/M981 clades than any of those clades is related to the Koryak (and Paleo-Eskimo, Sino-Tibetan, etc.) Q1a1-F746/NWT01. The TMRCA of Q1b1a-L54 is estimated by YFull to be 16,200 [95% CI 15,100 <-> 17,400] ybp, whereas the TMRCA of Q1-F903/L472 is estimated by YFull to be 26,000 [95% CI 24,200 <-> 27,900] ybp.

A finding of a deep divergence between Kets and Koryaks in regard to the ANE-derived portions of their genomes would fit with the deep divergence between Y-DNA haplogroups Q1b and Q1a under the assumption of a relationship between the spread of Y-DNA haplogroup Q1 and the spread of ANE autosomal DNA into North Asia and the Americas. However, I note that the ANE portion of the Ket genomes is indicated in Figure 3 to be the most basal, whereas the ANE portion of the Koryak genomes is indicated to share some additional drift with the genome of the Mal'ta specimen and with the ANE portions of the genomes of Native Americans and Eskimos.

Chad said...

Another gem with Northern Eurasians

https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-017-0578-3

Chad said...

I've got these new samples running through some ADMIXTURE runs now. About 6300 samples all-together.

Rob said...

@ Watkin

I don;t know too much about north America, however, in Europe, the very peak LGM (say, 25 - 18000 y BP) was a milder period thatn the period going into the LGM ((say, 30 - 25 kyBP). The peak LGM was just , as the name suggests, the peak extent of the Glaciation (and correspondingly lowest water levels). This was a period when recovery and (re-)connections began .

Ric Hern said...

@Chad

Very interesting. Thanks.

jv said...

@MomOfZoha,
Yes, hopefully this yDNA will help this researcher of this Surname. Some of the family claims to be from Scotland and some from England. Anyway my Great Great Grandpa Joel was born in Baltimore and was probably poor. However, this Surname was associated with Plantation/ land owners in Maryland. This reaseacher feels the 2 wealthy families may be related. I looked at project results and see one is R-M198 and the other is R-M512. Will interesting to see if my father matches one of these.

jparada said...

@MomOfZoha

[i]* Are there any Siberian groups that are "their own" highly divergent branch preceding the split between ANE and East-Asian? There were no such Siberian nor Native American groups so far in the graph so I doubt it, but the question remains.[/i]
There don't seem to exist such groups, and based on what we know from ancient DNA, i would say it's highly unlikely. The oldest known Siberian genome, Ust Ishim, is not significantly more divergent from ANE or East Asians than they are from each other, and besides doesn't seem to have contributed much to current Siberians. The oldest known genome from Europe, Oase1, is more or less the same except for extra Neanderthal admixture. The likelyhood of even more divergent groups living in Siberia is thus minimal.

[i]* Will all of the other indigenous Siberian groups *also* be admixtures of ANE and East-Asian branches, or not? Excluding Yoruba, so far only Mal'ta and Han are the "pure" nodes, corresponding to ANE and East-Asia respectively, which could have been part of the initial modeling assumption for the "seed graph". Koryaks and Kets share a sub-path of an East-Asian admixture branch but are on totally different ANE branches. Whether the answer to this question is "yes" or "no", I *really* wonder the resulting structure when nodes for other indigenous Siberian groups would be added to the graph.[/i]

ANE and East Asían seem so far to be the main contributors to Siberians/Native Americans, but this doesn't necessarily mean they are themselves unadmixed. ANE itself seems to be the product of admixture between East Asían and Palaeo-European related populations, and in its own turn seems to have contributed to modern East Asians. But these are details that don't affect much the fact that the populations in question can be modeled as ANE-East Asian mixtures pretty well.

pnuadha said...

@chad,

has the relation of ANE, EHG, and WHG been resolved at all? Is there actual ANE admixture in EHG. Also, can we estimate the levels of ANE in modern populations of Eurasia? I remember Davidski trying a while back but I dont remember much detail on how much ANE is in modern siberians and modern Asians.

Thanks

pnuadha said...

I see what Davidski thinks of these ancient groups

https://3.bp.blogspot.com/-1K7T5Rd4q8c/WWaoQFxZqwI/AAAAAAAAF3w/S5ziyr44K2M43QTRtBM8W34Bt-1HtWjDwCLcBGAs/s1600/Eurasia_1_qpGraph.png

pnuadha said...

@daviski,

When you computed the topography of Eurasian population structure did you use information on population bottlenecks?

In the mesolithic scandinavian paper they compare the bottleneck events in the lineages of WHG, SHG, and CHG. This looks like an important constraint on the topology of eurasian populations. Here is where they describe their finding During the Mesolithic, by contrast, we find higher levels of genetic diversity (Supplementary Information 7) as well as lower levels of runs of homozygosity (Fig. 2A) and linkage disequilibrium (Fig. 2B) in SHGs compared to WHGs (represented by Loschbour and Bichon, (15, 29)) and Caucasus hunter-gatherers (CHG, represented by Kotias
and Satsurblia, (29)). Using a sequential-Markovian-coalescent approach (30) for the high- coverage, high quality genome of SF12, we find that right before the SF12 individual lived, the effective population size of SHGs was similar to that of WHGs (Fig. 2C). At the time of the LGM
and back to c. 50,000 years ago, both the WHGs and SHGs go through a bottleneck, but the ancestors of SHGs retained a greater population size in contrast to the ancestors of WHGs who went through a more severe bottleneck (Fig. 2c). Around 50,000-70,000 years ago, the effective
population sizes of the ancestors of SHGs, WHGs, Neolithic groups (represented by Stuttgart (15)) and Paleolithic Eurasians (represented by Ust-Ishim (31)) align, suggesting that these diverse groups all trace their ancestry back to a common ancestral group which likely represents
the early migrants out-of-Africa, who likely share a common ancestry outside of Africa.

Davidski said...

@Colin

When you computed the topography of Eurasian population structure did you use information on population bottlenecks?

This shouldn't effect the qpGraph trees. I run the tests with "inbreed" YES, so all of the samples are inbred.

Ryan said...

Any idea how/why/where SHG maintained the larger population size?

MomOfZoha said...

@jv: Ah, the poor are disadvantaged even posthumously as there is far less recorded of them than their richer counterparts. However, it is my own family's experience that one can go from rich to poor or poor to rich so quickly between generations that things get confusing if we assume the stuff to be constant. For example, my materially poor maternal grandfather was disowned by his own materially rich father on account of the son's anti-religious rebelliousness -- apparently my vengeful great-grandfather even forced his poor son to pay him "nafaka" ("parent support payments") throughout his life as punishment. So, we lost a lot of the fascinating family history of my maternal grandfather (may he rest in peace) that I have only been able to partially reconstruct with DNA posthumously. It appears that they were very closely related to the Circassian Mamelukes of Iraq, along with definite Iraqi Kurdish and probable Ashkenazi Jewish (given a Ukrainian Jewish X-match, Latvian Jewish match, and Finnish-Polish Jewish match whose Polish-Jewish paternal ancestry is of Y-haplogroup N-M232) heritage mixed in. So, all of those semi-inconsistent family stories about my maternal great-grandfather's family having been "invited" by the Ottomans to Konya from "somewhere in Arabia" finally start to make sense (as well as, perhaps, my brother's red beard)...

@Ebizur and @jparada:
Thank you both for your highly informative replies. What I understand from jparada's reply is that many other Siberian groups will likely also appear as ANE-East Asian admixtures WLOG. What I further understand from Ebizur's reply is that at least some Samoyedic speaking peoples and Turkic speaking peoples may be hypothesized to share a sub-path of the Ket ANE branch if added to the graph so far. Please correct me if I misunderstood.

Both of my parents share > 5cM with a lot of Siberian populations, not only Turkic speakers like Tuvans but especially Uralic speakers and Samoyeds (e.g. my mom with Nenets-Tundra). I literally have to go now, but can't help asking: Where do Y-haplogroup N people fit into the picture so far, say restricted to present day Y-hg N Siberians?

Matt said...

@Ryan, pretty good question (Any idea how/why/where SHG maintained the larger population size?)

I would say bear in mind that it may not *literally* mean that there was an SHG like population that existed in the long term at a larger population size than a separate WHG population (so we don't necessarily have to think in counterintuitive ways of relatively large populations surviving in northern latitudes where survival may have been tough over a long term).

A couple ideas I have that may point to an answer:

1) There seems to be a general cline of nucleotide diversity from EHG to WHG:

https://imgur.com/VpFy2i9

Western WHG look to be the expansion from Villabruna and to some extent El Miron clades, so I'd guess they have a founder effect from both sets of ancestors which is reducing nucelotide diversity, and this is confounded with reduced ancestral population size in the "WHG" subclade of Villabruna cluster.

Iron Gates HG vs Scandinavia HG may be more "apples to apples" comparison.

2) On top of why that cline exists, as well as a founder effect effecting mainly Western WHG, I think there *may* be an effect where pooling ancestors from different populations gives greater ancestral population size.

That is, say population C is admixed from A with ancestral population 10,000 and B with 10,000, then C may have an ancestral population size >=20,000 - depending on how this hashes out but certainly greater than 10,000.

(Having an ancestral population size of X may not literally mean that all those X were evolving and reproducing together as a single panmictic population of that size.)

Since SHG seems to be Iron Gates HG/Villabruna+Eastern HG, and EHG *may* be late upper paleolithic ANE+Iron Gates/Villabruna, that may be part of the story?

El Miron related ancestry in WHG may not be boosting diversity as much because all the graphs indicate it was much less diverged from Iron Gate HG/Villabruna clade (compared to ANE).

....

Generally as well, this all may be why western WHG sometimes seems so much more extreme in its position relative to even the nearest ancient Near Eastern populations in PCA and Fst.

See here: https://i.imgur.com/6EH0poa.png

EHG is about 0.005 closer by Fst to Levant_N than WHG based mainly on Western samples is, and about 0.02 Fst closer to Iran_N! WHG is only closer than EHG to Early and Middle Neolithic European Farmers. Higher population size (through pooling of ancestors or low founder effects) = less drift away from both relatives and outgroups (hence African outgroups are also slightly closer to EHG than WHG).

(And on more of a tangent, in turn that may influence patterns in Yamnaya vs European_MN, where depending on the MN group chosen, MN tends to be quite a bit closer to its nearest ancient Near Eastern relative, Levant_N than Yamnaya are to Iran_N, but also slightly further away from Iran_N than Yamnaya are from Levant_N, and both equal distance from African outgroups: https://i.imgur.com/K3qS8Zl.png and https://i.imgur.com/BBNuOvY.png. Despite what we might intuitively assume about MN knowing only that it likely had less Euro HG ancestry than Yamnaya...

Perhaps by a loose comparison think of how the Uyghur have lower Fst distance to Yoruba (0.138) than say, Armenians (0.143), despite being pretty distant from Africa and the likelihood that many of their ancestors have been through harsher bottlenecks. However at the end of the day, Uyghurs pool a wider variety of ancestors through being in the centre of Eurasia, so in a sense can converge more back on the ancient African diversity that is lost by AMH in Eurasia through founder effects.).

Ryan said...

@Matt - "Having an ancestral population size of X may not literally mean that all those X were evolving and reproducing together as a single panmictic population of that size"

I think that depends on linkage disequilibrium. Is there even evidence of that in SHG? Are they clearly admixed, or just a point on a cline? (I'm sure some paper has checked this I'm just asking does anyone remember the result).

Anyone have the proper name of the paper that Colin is referring to?

Matt said...

@Ryan, it would pretty cool if anyone could use that data in SHG or EHG. As I understand it, no one seems to have tried to use LD admixture methods for the populations on the WHG->EHG clines (rather than simply various forms of modeling that assume admixture, and f3 admixture stats to test admixture). I don't know if there's enough in the data for them to work with there. I think it's highly, highly unlikely that they are anything but a mixture of the Villabruna and EHG groups (though there may be a bit of substructure within those pops as well to consider) but I can't say that it has been shown through LD.

Googling of the excerpts in Colin's post indicates this paper is "Genomics of Mesolithic Scandinavia reveal colonization routes and high latitude adaptation" - Gunther 2017. (They go with a model of ancestral admixture of course, "These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments.", but no ALDER type tests that I can see.)

Kristiina said...

@MomOfZoha ”Where do Y-haplogroup N people fit into the picture so far, say restricted to present day Y-hg N Siberians?”

It is not only in Siberia: http://www.cell.com/action/showImagesData?pii=S0002-9297%2816%2930160-4. However, the oldest forms seem to be in Western Siberia and South Siberia.

The ancient N record is scanty; probably because very little ancient DNA is available from the relevant areas.

Scythian Pazyryk Culture of Southern Siberia has yielded two N1b males who probably were Turkic speakers (https://www.researchgate.net/publication/301548191_Pilipenko_2015_A_PALEOGENETIC_STUDY_OF_PAZYRYK_PEOPLE_BURIED_AT_AK-ALAKHA-1_THE_ALTAI_MOUNTAINS_in_russian).

In December, a paper on Western Siberian Sargat Culture was published. This analysis yielded 2 x R1a1 and 5 x N1c1. N1c1 is under Z1936, i.e. it belongs to the Western clade. These men were probably Uralic speakers or more specifically Ugric speakers. (https://www.researchgate.net/publication/321071660_Kinship_Analysis_of_Human_Remains_from_the_Sargat_Mounds_Baraba_Forest-Steppe_Western_Siberia).

Rob said...

Kristiina
Don't forget IR1

Kristiina said...

@Rob Yes, that's right, and he is from the pre-Scythian Iron Age Mezőcsát culture of Hungary. However, his linguistic affiliation is less clear. He was found in the Cimmerian context, and according to Wikipedia "There is a tradition in archaeology of applying Cimmerian to the archaeological record associated with the earliest transmission of Iron Age culture along the Danube to Central and Western Europe, associated with the Cernogorovka (9th to 8th centuries) and Novocerkassk (8th to 7th centuries) between the Danube and the Volga".

According to Genetiker, RISE554 from the Iron Age South Siberian Afontova Gora site belongs to the same line as Ir1. This line is still found in the Balkans but the original population and its language have probably disappeared as the line is very rare today.

Michalis Moriopoulos said...

Great paper, but I'm puzzled by how long it's taking to get a truly diverse sampling of North American Amerinds. Central and South American coverage is pretty good, but the record for natives living in the States is conspicuously poor. We've got stuff from the Pacific Coast and the Southwest, but what else? Autosomal DNA from the Great Plains and Eastern Woodlands is virtually non-existent, save for a few Algonquins. And considering their renown and historical importance, it's strange that the Sioux, Cherokee, and Seminole have yet to be sampled. Siouan-Catawban, Iroquoian, and Muskogean tribes are hardly fringe groups and deserve genetic representation. Hopefully their absence in the record will be rectified soon.

I'm not sure if any of you were aware of this, but in 2016 the US Congress in its infinite wisdom decided to allow Native American groups to "re-bury" Kennewick Man. Thankfully we got his DNA before that happened, but it's still depressing to know how easily superstitious protestations trump scientific interest. The Kennewick specimen is no longer available to us should we ever need to look at it again, and all because we felt the need to appease the base desires of people who would rather wallow in religious drivel than try to understand the world as it really is.

---

Moving on to something else:

I've seen the Kets modelled in this paper (and several others) as a simple mixture between ANE and a Siberian form of East Asian which peaks in Nganasans. Some Kets show low amounts of "southern" EEF or CHG ancestry (perhaps consistent with recent Russian admixture), but there are several "purer" examples that don't seem to have any at all. This might also be the norm for Selkups, Nenets, and Yukaghirs. I would like to pose this question: are we right to accept this two-component mixture scenario or is there more to the story?

The Flegontov paper on the Kets suggested they might have a connection to the Early Bronze Age Okunev and the Late Bronze Age Karasuk culture. I'm not sure about Okunev, but Karasuk shows clear evidence of EEF/CHG ancestry consistent with ancient steppe admixture from Andronovo. Again, I've seen no evidence that Kets have these "southern" components; if their ancient Yeniseian forebears did in fact have them, why don't they? Or are they indeed survivors of an ANE-East Asian admixture event that almost totally avoided steppe introgression?

Lee said...

@Mike the Jedi. Difficulties in obtaining Native American samples stems from NAGPRA and a general distrust of many Native americans of "european" scientists.

Kennewick man-once determined to be a relative of existing Native American tribes, Was subject to control by NAGPRA. The native american tribes have full rights to control and protect the remains of their ancestors. Just because it is inconvenient to science and western culture may not have the same type of ways of expressing respect for ancestors, we as a community must respect the cultures of those people we have interest in.

Ultimately, scientific curiosity does not outweigh the cultural rights of people. I wish that northern native americans, in general, were more open to free scientific investigation. But they have a well earned distrust of "europeans". In the Northwest, the Willserlev group has done a lot of good work in gaining partnership with Northwestern tribes. This includes agreements to restrict access to much of the genetic information they obtain. Most northern native american sequences are sequestered and require special permissions to access. Again, individuals have rights to control their own genetic information. I personally consider that a basic human right of everyone.

Michalis Moriopoulos said...

Sorry, Lee, you can speak for yourself on this one. I am under no obligation to respect any idea I find insulting to my intelligence. If the remains under NAGPRA's "protection" were recent relatives of people living today, I wouldn't take much issue with it. But it also covers ancient remains. It's not like "European scientists" headed over to Indian burial ground and started digging up Grandma Sitting Bear. The real reason NAGPRA exists is because there is an industry of grievance and outrage in the West that has been championed by misguided activists for some time. We'll indulge any Native American interest groups with an axe to grind because we feel sad and guilty about what happened to their ancestors. Natives have a very tragic history, yes, but that doesn't justify any bad ideas they might have now. Anthropology has no business pandering to retrograde beliefs that assert racial ownership of fossils and material culture, let alone religious protestations. It should be above such parochial, anti-scientific inanity. I don't want to seem callous to Amerinds, but as an anthropologist I feel just as strongly about the importance of science as the other side does about repatriation.

Ethnic ownership. That's what we've been pressured to accept here when you really think about it. The fact that Kennewick Man has continuity with Pacific Northwest tribes should mean fuck-all. He doesn't belong to them anymore than the Mycenaean remains belong to me. If the San demanded we "give back" Ballito Bay Boy ("He's our ancestor; you must respect our religious beliefs about burial!"), we'd tell them to suck it up. If some Italian Catholics complained about the recent testing done on that medieval Lombard cemetery in Italy ("It's un-Christian; put them back!"), we'd tell them to get lost. If West Africans protested testing of ancient Nigerian fossils because of, say, Pontus Skoglund's Basal Human hypothesis ("Europeans are trying to prove we're the most primitive!"), would we entertain them? I doubt it. So why then should I happily accept that ancient Amerind fossils are unfit for the laboratory? Because history dealt their descendants a particularly bad hand? No, I'm not playing that game. Every ancient fossil should be subject to the same ethical considerations as any other, no matter where in the world it came from. I respect the common humanity of homo sapiens too much to cater to any short-sighted, anti-scientific mentalities that some of its members might happen to harbor at present. Kennewick Man belongs to the world, and in that sense he's just as much a part of my heritage as he is anyone else's.

As far as genetic rights of Native Americans who don't want to be genotyped, of course they can refuse. But it's as much their loss as ours.

Samuel Andrews said...

@Mike Jedi,
"If the remains under NAGPRA's "protection" were recent relatives of people living today, I wouldn't take much issue with it."

That's the thing. These tribesmen & politicians are ignorant of some basic historical knowledge. To them 10,000 years or 500 years makes no difference. They think Kennwhich man belonged to the same tribe and followed the same burial traditions. Somebody's got to educate these people.

Thanks for mentioning you have no problem putting limits on recent remains. It seemed like you were calling for no limits at all. Please, keep in mind that to most of society a hero, a saint, a founding father has more value than anthropology. Anthropologist should not be allowed to mess with whatever they want to for the cause of whatever their interest area is. I don't beleive laws should be put in place because every situation is different. What should happen is the people who for whatever reason don't want something digged up should give given an avenue for requesting a stop to the dig.

"If West Africans protested testing of ancient Nigerian fossils because of, say, Pontus Skoglund's Basal Human hypothesis ("Europeans are trying to prove we're the most primitive!"), would we entertain them? I doubt it. So why then should I happily accept that ancient Amerind fossils are unfit for the laboratory? Because history dealt their descendants a particularly bad hand? No"

Yep, there is a double standard.

Chad said...

You guys get into this race-baiting shit on your own. No "lefties" needed. If you guys can't wrap your head around cultural competence and respect for others, don't expect any respect back.

Ric Hern said...

@Mike the Jedi

I partly agree with you. If future studies can pinpoint more accurately to which tribe remains of an ancient actually belongs, would it not be a disfavour to that specific tribe if the remains are buried prematurely by a different tribe ?

Yes that tribe may not be any wiser because there were no proof at the time, but would this be moraly just ?

I'm specifically thinking here of potential Land Claims and who were where first...etc.

For example there are talks about pushing back the date of claims back to the 1600s.in a specific country. Between the 1600s and the present there were a lot of internal displacements and political turmoil amongst tribes....Burying remains by one tribe could be used as a political playball to hide the truth about another tribes actual history and claim to land...

Michalis Moriopoulos said...

Chad, I'm actually a left-leaning liberal myself, but I'm also committed to scientific enterprise and have little patience for those who would needlessly undermine it. "Ownership by blood" of ancient remains of scientific interest strikes me as quite racist actually, and that's partly why I find NAGPRA so distasteful.

Also, just follow re-burial to its natural reductio ad absurdum. Imagine if some NatAm group lobbied for Mal'ta Boy to be re-buried. After all, he belonged to a population making up an astounding 40% of the ancestry of Amerinds. Should we honor the request? No? Why not? Because ANE lived in Siberia and not America? Does our "respect" for NatAm concern for their ancestors' spirits end at the Bering Strait? Hey, I'd love to be culturally competent and respectful, but I can't help but feel like this shit don't make a whole helluva lotta sense.

I'm glad we have Clovis and Anzick and now URS1, but if any interest group at any time could lay claim to these remains and be taken seriously by Congress, is it any wonder why some of us might find that more than a little ridiculous? I was hoping we'd all be on the same page here. If wishes were horses.

Michalis Moriopoulos said...

Sorry to have gone on a Kennewick Man bender, but it is after all a pretty important subject and relevant to any study of American Indian remains.

Getting back to the implications of the paper at hand, it's nice to have an upper and lower bound for the colonization of the New World. The early date for the Monte Verde site in Chile cuts a bit close to the time of the estimated North/South Amerind divergence, but it looks like we're closing in on a date here. Archaeologists should be probably pretty excited about that since they've been arguing about the dates for a while now.

I hope that the mystery of the ostensible Australasian gene flow into the Amazon and the late Fuegians is also resolved in the near future. If Luzia made an appearance in the aDNA record, that would probably make my year!

Matt said...

Glad we don't yet have people in reality complaining about Eurocentricism of ancient dna, and advocating at the same time that populations coordinate to prevent being sampled, or specific remains being sampled.

Now, on this topic, we have a pretty good understanding on the origins of Native American peoples, and the main consequence of the holes in the sampling is that specific people is that they have less understanding of the real history of their ancestors (than other Native American people and other people generally), and that, probably more concretely, we will have less understanding of their disease and health genetics. which in time will have consequences mainly for them.

So restriction of data will mainly have consequences for the people themselves. (Partly, thankfully, in particular because these are very peripheral groups).

Without having given it a lot of thought, I guess I'm mostly fine with that (I'd certainly grumble more if it was holes in Africa, SE Asia or the ME, more critical regions for the species history). But hope the people who are advocates for delegating these choices to selected representatives of Native American groups understand these consequences. More than that, that they understand their responsibility to explain those consequences, and that giving this choice means that it could well leave those people worse off in some ways, feeling simplified within the real genetic history of our species and less well understood in genetic medicine, and are willing to say "Yes, I am the one responsible, and my political approach was responsible for this outcome." if those consequences play out.

(Don't like politics on this blog, but in this instance felt like there's enough overlap with the blog topic to be worth it).

pnuadha said...

@Davidski This shouldn't effect the qpGraph trees. I run the tests with "inbreed" YES, so all of the samples are inbred.

I was more so thinking of it as a way of checking your work. It seems to be an added piece of information.

MomOfZoha said...

Thank you, Chad and Lee.

I would like to add that the distrust of the Natives may be compounded by anthropology's unfortunate track record -- even in the most recent history -- when it comes to "measuring" people, not only non-Europeans but even Poles and Ashkenazi for that matter. Since volumes have been written on that, I don't think I need to further clutter this space about it. However, I just want to point out that the Turkish argot word for "fascist" is "kafatasci" -- literally meaning "skull-measurer"...

@Kristiina:
Thank you so much for that information. Especially the first paper that you have linked is fascinating, e.g. what is observed concerning Y-hg N3a3'6. I need more time to read the whole thing carefully. BTW, although my DNA-tested family does not exhibit Y-hg N, it is a haplogroup that has curiously come up in close matches, some of whom have initiated communication with me (hence garnering my notice), and I brought it up here as it relates to Siberian populations too. Interestingly, one of the haplogroup N people who contacted me was an Alevi Kurmanji (Kurdish) speaking individual from Elbistan who matched my Iranian Azeri father-in-law... My paternal grandmother's village Afshar was also likely Alevi before the time of the Ottoman Selim, and my father has a very close match with another Y-hg N (with ~15% total Siberian + East Asian component) from his own province Konya....

Onur Dincer said...

While off topic, nevertheless of huge significance:

http://www.hurriyetdailynews.com/turkish-scientists-to-crack-neolithic-era-dna-code-european-funding-awarded-125398

Some highlights:

"The European Research Council (ERC) has awarded Turkish scientists a €2.5 million ($2.9 million) grant to analyze the DNA of 1,500 people who used to live in the Anatolian region – the Asian part of present-day Turkey – during the Neolithic period."

"“During the study, genetic samples, which belong to almost 1,500 people from 20 Neolithic Anatolian settlements, are set to be scanned using a DNA sequencing method.”

The study will then narrow down its research to focus on 350 people, whose samples will be subject to deeper analysis.

The second stage of the study will devote itself to bioinformatics analysis to determine genetic proximity and gene flow among communities."

Matt said...

@Onur, could really be more novel the more eastern Anatolian they go. So far in Anatolia in the Neolithic, I think we have distinct groups of a) Boncuklu Central Anatolia, b) Barcin and Mentese NW Anatolian and c) Tepecik-Ciftlik Central Anatolia.

The Barcin and Mentese NW Anatolian seem like the typical EEF group, minus some WHG, while Boncuklu are distinct mainly by seemingly having far less heterozygosity and nucleotide diversity (a much more bottlenecked or narrower pool of ancestors, which to me suggests they were from mostly local small group of foragers, unlike Barcin who had a more genetically diverse pool of Boncuklu like ancestors) and the later Tepecik Ciftlik group are distinctly modeled as clinal with the Levant and CHG (estimates in Lazaridis 2017: 24% CHG, 9% Levant N).

For one, further eastern groups might begin to get us closer to better proxies for Near Eastern actual ancestors for Eneolithic and early Bronze Age groups from the Pontic-Caspian steppe (and Armenia CA).

Onur Dincer said...

@MomOfZoha

I would like to add that the distrust of the Natives may be compounded by anthropology's unfortunate track record -- even in the most recent history -- when it comes to "measuring" people, not only non-Europeans but even Poles and Ashkenazi for that matter. Since volumes have been written on that, I don't think I need to further clutter this space about it. However, I just want to point out that the Turkish argot word for "fascist" is "kafatasci" -- literally meaning "skull-measurer"...

While you have a point there regarding the past mistakes in the application of skull measuring and its interpretation, skull measuring is still a widely applied practice in scientific studies and should not be disregarded wholesale. Having said that, genetic clustering methods should always be preferred to skull measuring in ancestry research as they are much more directly related to ancestry and much less prone to misinterpretation. Also, I prefer genetic clustering-based categories such as West Eurasian, East Eurasian, Sub-Saharan African, Amerindian, Oceanian and ASI to closely related but skull measuring-based categories such as Caucasoid, Mongoloid, Negroid, Amerindoid, Australoid and Veddoid as the latter are outdated and somewhat misleading (West Eurasians did not originate solely in the Caucasus and Mongols are far from being pure East Eurasians, etc.).

Davidski said...

@Matt

There's an nMonte3 available now, with an option to vary a penalty (pen) ratio. Might be worth testing.

https://www.dropbox.com/sh/1iaggxyc2alafow/AACIjLtnkuaNNsJ5oKME_3XHa?dl=0

CleverPrimate said...

MiketheJedi,
In my opinion it's not off topic or inappropriate to discuss the Kenniwick Man controversy on this thread. As you may note from my initial comment, upon first reading this post my first thoughts were how these new genomes compare to Kennewick man and what new information about the peopling of the New World will be gained from the comparison. I agree that the genetic picture of the Native Americans of North America is unnecessarily sparse. I think that the NAGPRA as it currently stands contributes in no small part to the paucity of available information and will continue to have a chilling effect on research as long as it remains in place. What researchers are going to invest the time and resources towards making new discoveries in this field knowing that anything they may discover will be seized and impounded as Kennewick Man was and then turned over to parties whose connection to the materials discovered may be dubious and debatable, and who will re-inter any human remains discovered with no possibility for further expert examination.

Unknown said...

@Lee Albee

The coast was largely glaciated - similar to eastern Greenland today And while I take your point about lower sea levels, I'm still struggling to see that such a journey was feasible with the technology we understand to have been available.

Inuit technology was not primitive - in fact the Inuit conquered half the Arctic with it - seeing off the Dorset people, Native Americans and then the Norse. They also colonised areas that were previously uninhabited.

In particular, the Inuit relied on very sophisticated kayaks and compound harpoons. Neither of which are considered to have been available at 20,000 BCE.

As regards boats, conventional wisdom dictates that you had a choice of wood or reed rafts, animal skin coracles or dugout wooden canoes. None of which would have been much use in the northern Pacific ocean during the LGM - even for hopping along the coast. And Beringia didn't even have any trees.

Without a two piece harpoon with floats attached (quite possibly an Inuit invention), hunting whales is near impossible. The same for other large sea mammals - with the possible exception of seals.

Of course we don't know exactly how the people of Beringia lived, but they were most likely big game hunters - as were the ANEs who joined them at the peak of the glaciation from Siberia. So for them to develop maritime technologies not seen elsewhere for thousands of years would be quite surprising - especially since there is no evidence of sophisticated maritime technology in north America after "the great leap south". In fact the early (pre-Clovis) archeology is characterised by big game hunting using relatively simple stone tools.

So I still think there is a missing piece to the puzzle. But I doubt its the genetics - which seems pretty clear cut now as regards both the date and principle source population for the colonisation of north America.

Matt said...

@Davidski late to reply. Thanks. I've had a look at the new nMonte and Ger's comments on it. I kind of understand the goals of it, and there are some defined benefits and penalties depending on the situation you're using it for, with the penalty ratio and post-run averaging step. Really to help it to try and place a new sample as a member of an existing populations that are sampled, even when the raw distance would be better fit by averages of two more distant populations.

That said, I don't really see myself using it any time too soon, as those aren't the kind of scenarios I'm looking to run at the moment. (To honest, for the scenario I've described, trying to fit a sample into the best one population that you have, I'm not sure I wouldn't just use Linear Discriminant Analysis clustering on the PCA data with all the samples, or just use a neighbour joining method on the distance matrix or squared distance matrix... I'll have to think about that some more).

MomOfZoha said...

Selam Onur:

While I am happy that we at least agree on some of the unfortunate effects of "kafatascilik", I prefer to take a more principled approach beyond simply allowing something as long as it doesn't definitively cause harm directly.

When scientists take an un-principled "oh what's the harm?" approach, what happens is that there arises no true disconnection, no discontinuity, between the truly racist "scientists" who preceded them and themselves. While not necessarily "racist" themselves, they become the intellectual descendants of the scientific racists.

The particular classification to which you directly refer was most popularized by Coon just a few decades ago (not to detract credit from Blumenbach's original lust for Kartvelian skulls the previous century), and Coon was a definite segregationist. You yourself are aware of the "Turkish bone" kafatasci shitheads of the 1970s -- how great it would have been to have forced them all to DNA tests whereby many would discover their Armenian and Kurdish ancestries...

So, forgive me that I cringe every time I read a paper talk about "Mongoloid" versus "Caucasoid" skulls (getting all confused by those pesky dolicocephalic Mongolians and brachycephalic Caucasians), no matter what the authors' intent. I am sure that authors of such modern works are only trying to convey as much information as necessary in the anthropological language that they have been taught.

Let us return to the issue at hand, Native Americans: A people killed by police at a higher rate than any other ethnic group; their women the most vulnerable targets for rape; and their poverty limitless...

What has anthropology ever done for them (other than repeatedly taking not only their beloved objects but also the discovery credit itself away from them)?

Adding insult to injury, Utterers of Fake "Namaste"s around here make fun of the only solace such a deprived people have remaining -- their spirituality. A spirituality that has connected indigenous people to their natural surroundings and fellow living beings millennia before evolution gave scientific grounding to our inherent connectivity. A spirituality that -- *unlike* every organized imperialistic religion (including that of my own ancestors) -- has *not* compounded the totality of human pain.

So, instead of pretending that the Natives "owe" anything to "science" -- a "science" which is the direct product of allegedly "scientific" human beings -- perhaps some scientists should humble themselves and question what they could do with true respect instead. Organizations like NAGPRA are bandaids on amputated limbs. If only some scientists would care as much about the living, breathing indigenous people today as they care for millennia old indigenous remains, prosthetic limbs might be possible for a real solution after all...

Onur Dincer said...

@MomOfZoha

The historical misuse of the -oid terms aside, I find them flawed on scientific grounds as I explained in my previous post. Geographical terms that make genetic and (pre)historical sense are much more accurate to define the clusters of mankind we find based on genetic and/or physical anthropological studies.

Yes, crackpot ideas such as Turkish/Turkic/Turanic bone or brachycephalic race have no place in science. Brachycephaly is a common trait found in almost all parts of the world and cannot be used alone to define a genetic/racial cluster within mankind.

I think American authorities should make a distinction between skeletons of people with known genealogical ties to some living people and skeletons of people with no known genealogical ties to any living person and should enforce consent only in the former case in DNA sampling and other skeletal studies. This is the usual practice in much of the world, no exception should be made for any specific community regardless of ancestry or history.

NKent805 said...

Early UpperPaleolithic people of Europe were nothing like The Inuit. They were Hunters and had no experience in Artic living, unlike the Alaskan people and early Native Americans. Solutreans were from the southern latitudes, even as far south as North Africa. Yeah they could of, but they also could of flown a glider over the Atlantic ice sheets.

NKent805 said...

Americoids , since they were a isolated breeding population for far longer than Europeans and Asians , they are a continental race.

NKent805 said...

well since Europeans have only been in the Americas for a few hundred years they have no rights to the cultural patrimony and remains, of the Native Americans. Being a recent immigrant to the Americas you have no ancient history, and you are not entitled to the history prior to European mass immigration. Its against the law, and thats all you need to know. get over it.

NKent805 said...

Blood and soil only applies to Europeans in Europe. it does not apply to European immigrants to the Americas. Blood and soil applies to the Ethnic Americans, the Native americans in their ancestral Na homelands.

NKent805 said...

Duh! Native Americans dont give a shit about customized genetic medicine. They survived and thrived for thousands of years in thr Americas without it, dont flattet yourself in regards to their DnA.

NKent805 said...

you are forgetting the advanced maritime tech of the ancestors of the Chumash indians in the Santa Barbara Channel islands and san Nicolas 60 miles of the coasts of central and Southern Califoria, there are hundreds of offshore archaeological sites that date back 14,000 years. The Chumash were the only people to make atrue planked Boat.