Wednesday, December 12, 2012

Efficient moment-based inference of admixture parameters and sources of gene flow




Luis, you have to check out this new MixMapper paper.
The method employs a concept called scaffolding within a moment method.

There's an interesting discussion about the employment of f2 distances versus genetic drift D statistics, which I'm sure, you, Luis, will want to read. (See "Expressing branch lengths in drift units."). There's also a good discussion of ascertainment bias in the "Data Set" section.

Also, unsurprisingly, it appears that it is actually quite difficult to find populations that have little admixture: "Despite the focus of the HGDP on isolated populations, most of the 53 HGDP groups exhibit signs of admixture detectable by the 3-population test, as has been noted previously (Patterson et al., 2012)." And in the end, these researchers can find only 20 populations that are potentially unadmixed.

Regarding Europeans, there are virtually no unadmixed populations. But, on the bright side, Luis, apparently among Sardinians and Basques, there are 20-25% “ancient northern Eurasian” allele frequencies.

Other very interesting results are that the Daur, Hezhen, Oroqen, and Yakut—are likely descended from admixtures between native North Asian populations and East Asian populations related to Japanese.

Also interesting: "we found that Han Chinese have an optimal placement as an approximately equal mixture of two ancestral East Asian populations, one related to modern Dai (likely more southerly) and one related to modern Japanese (likely more northerly), corroborating a previous finding of admixture in Han populations between northern and southern clusters in a large-scale analysis of East Asia (HUGO Pan-Asian SNP Consortium, 2009)."

And corroborating various mtDNA, y-DNA, ADMIXTURE results: "Mozabite, Bedouin, Palestinian, and Druze, in decreasing order of African ancestry, are all optimally represented as a mixture between an admixed western Eurasian population (not necessarily European) related to Sardinian and an African population (Table 3)." 

I have a friend who is a Berber who is proud of her partly African ancestry . . . she told me so, not even knowing anything about these genetic studies.

Oh, and check this out: "Orcadian to an ancestor of Americans." Score one for the "Across Atlantic Ice" hypothesis. I'll have to add Dennis' book to my book list.

Way to go, MIT!

Here's the paper:

Efficient moment-based inference of admixture parameters and sources of gene flow
Mark Lipson, Po-Ru Loh, Alex Levin, David Reich, Nick Patterson, and Bonnie Berger
http://arxiv.org/abs/1212.2555


"[We] introduce MixMapper, a new computational tool that fits admixture trees by solving systems of moment equations involving the pairwise distance statistic f2 (Reich et al., 2009; Patterson et al., 2012), which is the average squared allele frequency difference between two populations. The theoretical expectation of f2 can be calculated in terms of branch lengths and mixture fractions of an admixture tree and then compared to empirical data. MixMapper can be thought of as a generalization of the qpgraph package (Patterson et al., 2012), which takes as input genotype data, along with a proposed arrangement of admixed and unadmixed populations, and returns branch lengths and mixture fractions that produce the best fit to allele frequency moment statistics measured on the data. MixMapper, by contrast, performs the fitting in two stages, first constructing an unadmixed scaffold tree via neighbor-joining and then automatically optimizing the placement of admixed populations onto this initial tree. Thus, no topological relationships among populations need to be specified in advance.

"Our method is similar in spirit to the independently developed TreeMix method (Pickrell and Pritchard, 2012). Like MixMapper, TreeMix builds admixture trees from second moments of allele frequency divergences, although it does so via a composite likelihood maximization approach made tractable with a multivariate normal approximation. Procedurally, TreeMix is structured in a “top-down” fashion, whereby a full set of populations is initially fit as an unadmixed tree, and gene flow edges are added sequentially to account for the greatest errors in the fit (Pickrell and Pritchard, 2012). This format makes TreeMix well-suited to handling very large trees: the entire fitting process is automated and can include arbitrarily many admixture events simultaneously. In contrast, MixMapper is designed as an interactive tool to maximize flexibility and precision with a “bottom-up” approach, beginning with a carefully screened unadmixed scaffold tree to which admixed populations are added with best-fitting parameter solutions.

"We use MixMapper to model the ancestral relationships among 52 populations from the CEPH-Human Genome Diversity Cell Line Panel (HGDP) (Rosenberg et al., 2002; Li et al., 2008) using recently published data from a new, specially ascertained SNP array designed for population genetics applications (Keinan et al., 2007; Patterson et al., 2012). Previous studies of these populations have built simple phylogenetic trees (Li et al., 2008; Sir´en et al., 2011), identified a substantial number of admixed populations with likely ancestors (Patterson et al., 2012), and constructed a large-scale admixture tree (Pickrell and Pritchard, 2012). Here, we add an additional level of quantitative detail, obtaining best-fit admixture parameters and bootstrap error estimates for 30 HGDP populations, of which 20 are admixed. The results include, most notably, a significant admixture event in the history of all sampled European populations (Patterson et al., 2012), among them Sardinians and Basques."

29 comments:

  1. "we found that Han Chinese have an optimal placement as an approximately equal mixture of two ancestral East Asian populations, one related to modern Dai (likely more southerly) and one related to modern Japanese (likely more northerly), corroborating a previous finding of admixture in Han populations between northern and southern clusters in a large-scale analysis of East Asia"

    Luis won't like that bit especially. I've been trying to tell him for years that south Chinese and SE Asians are a mix of a northerly 'Mongoloid' people overlaying an earlier 'Papuan' population. He just cannot see it.

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  2. Hi Terry,

    I would be very cautious in drawing any absolute conclusions about the sources of population admixture here. I think the paper is providing a kind of vector for the sources of admixture, but even the authors themselves admit that their referenced populations are "potentially" admixed.

    Also, the method currently allows for up to only three ancestral waves of admixture. It is likely that IBD segment scaffolding embeds many more than three admixture events.

    Luis got on my case last night by email about the 20 to 25% ancient admixture in Basques and Sardinians. In fact, I would agree with him that it is higher, but the higher level is likely obscured by variouy forms of ascertainment bias.

    He also scolded me about the Solutrean hypothesis.

    So, nice paper, but no conclusions on ancestral populations should be conclusively drawn from it.

    Again, the primary purpose of the paper is to improve population analysis methods.

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  3. "It is likely that IBD segment scaffolding embeds many more than three admixture events".

    Almost certainly so. Unlike some (who shall remain nameless, but I'm sure you know who) I do not subscribe to the theory that 'modern' humans left Africa in a single migration and swept through the world immediately occupying all of Eurasia south of the Himalayas. I strongly suspect that populations of humans, both ancient and modern, have been moving around much more than we are usually prepared to assume. Certainly more than most other species are capable of. The replacement of 'Archaic' human groups who had become geographically isolated is the product of that process. They were simply outnumbered by the many waves of humans able to enter the regions where the Archaics had been isolated long enough to now be classified as being separate species.

    "He also scolded me about the Solutrean hypothesis".

    I am very doubtful of the Solutrean hypothesis. The claim is that humans were able to move along the edge of the glacial ice to North America. It is very doubtful they would have found enough food to sustain them on such a trip, and it would have been even colder than was contemporary Siberia.

    ReplyDelete
  4. Terry, it's always interesting to hear your comments. Yes, I agree with the idea that humans, ancient and modern, have been moving around more than we have usually accepted.

    Luis sent me quite detailed descriptions of mtDNA X and Y-dna Q distributions. He argues that mtDNA X and Y-dna Q are "unmistakeably Western." However, many of the groups with high mtDNA X concentrations are associated with canoing cultures, and therefore, with high mobility.

    Algonquian peoples, a huge indigenous North American group, have high concentrations of haplogroup X. Many of these groups are associated with canoeing culture. For example, see:

    We Still Live Here (the story of the Wampanoag to recover their language): http://www.makepeaceproductions.com/wampfilm.html

    Intersection Ojibwe:
    http://intersectingart.umn.edu/


    As well, the Nuu Chah Nulth, (also Nootka), on the west coast of Vancouver Island are a famous ocean going canoe culture. Here's their tribal council page: http://www.nuuchahnulth.org/

    Again, canoe cultures are highly mobile, so I think the Solutrean hypothesis or "Across Atlantic Ice" hypothesis is an open question.

    You can also have a look at the pages for the "Paleoamerican Odyssey" conference which will be held next October 17-19th in Santa Fe, New Mexico. Most of the abstracts are already posted, so you can dig through the topics that are going to be discussed well in advance.

    http://paleoamericanodyssey.com/index.html

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  5. Thanks for those links. I'll check them out.

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  6. Regarding high mobility, I'll add this:

    I was recently reading about the early contacts of the La Verandrye expeditions with indigenous peoples: The Assiniboine, Cree, Mandan, Blackfoot and other groups.

    At least with the Assiniboine, they spanned the entire Canadian prairie, from Mount Assiniboine in the Canadian Rockies, to the Lake of the Woods, which touches Ontario. This is a distance of over a thousand miles.

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  7. "Luis sent me quite detailed descriptions of mtDNA X and Y-dna Q distributions. He argues that mtDNA X and Y-dna Q are 'unmistakeably Western.'"

    I completely agree with him on that.

    "Algonquian peoples, a huge indigenous North American group, have high concentrations of haplogroup X".

    That is extremely interesting. I don't know if you've ever seen this old paper on American Native haplogroups. I'm sure you'll find it interesting if you can find the complete paper. I can't seem to access it at the moment:

    http://www.ncbi.nlm.nih.gov/pubmed/10053017

    The gist of the paper is that Y-DNA Q spread to America from the ancestral population that gave rise to the Ket and Selkup people. Along the way they picked up women with East Asian affinity such as A, B, C and D. From that arises the concept that X was part of the 'original' Q people. If so X would be amoung the first women to enter America, but from the west. If that is accepted then we must conclude that the haplogroup got stranded in the northeast but has been able to expand from there more recently, possible as a result of their adopting an efficient canoe:

    "However, many of the groups with high mtDNA X concentrations are associated with canoing cultures, and therefore, with high mobility".

    "As well, the Nuu Chah Nulth, (also Nootka), on the west coast of Vancouver Island are a famous ocean going canoe culture".

    Do they have a notable level of mt-DNA X though? I suspect they have a high proportion of mt-DNA B.

    ReplyDelete
    Replies
    1. I have seen the paper.

      I grew up in British Columbia, my Dad grew up in Alberta and my mom grew up in Manitoba. I also have relatives in Saskatchewan. I went to school in Ontario and two of my grand parents are from Quebec. All of these provinces have vibrant, intact First Nations. That is not to say that there are not land claims issues or social injustice issues between First Nations and the various governments. However, First Nations people of Canada have increasingly negotiated their way into the mainstream of Canadian and American culture. Many are very well educated.

      Regarding the Nuu Chah Nulth, I believe they do have mtDNA X, but at a lower level than many Algonquian people.

      Delete
  8. By the way, are you of native American ancestry?

    ReplyDelete
    Replies
    1. None that I know of.

      I have a good friend that is part Wampanoag. My MASc thesis supervisor's mother was an Ojibwe.

      Living in British Columbia or Alberta, it is hard to miss First Nations culture. It's all around you.

      Delete
  9. "Living in British Columbia or Alberta, it is hard to miss First Nations culture. It's all around you".

    Canada does seem to have established better relationships with the First nation people than has the USA. I live in New Zealand and we also have a prominent indigenous culture. I recently did my teacher training and, of course, a significant element was teaching Maori children (rangitahi).

    "That is not to say that there are not land claims issues or social injustice issues between First Nations and the various governments".

    Same in this country, however progress is being made (I hope).

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  10. Woah. Amazing. Ever see the movie "Once Were Warriors"? Or read the book "English Passengers"? Where in New Zealand did you teach? I've been there. Sadly, North Island only. I got a really good sunburn in Tongariro National Park.

    If you're up for it, it would be terrific if you would write about your experiences teaching there. Maybe add some photos. You could put it up on Google blogger and I could link it. We could all learn something.


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  11. "Where in New Zealand did you teach?"

    Several schools in Whangarei, about 2 hours north of Auckland. I actually teach just guitar, so it is nowhere near as stressful as classroom teaching.

    I have seen 'Once Were Warriors' but not read the book you mention. 'Once Were Warriors' was written by a Maori to draw attention to the behavour of some of his people. I'm not sure if it worked but the film was reasonably popular.

    I'm not very computer literate I'm afraid but I'll see what happens.

    By the way, I was distracted yesterday and I meant to point out that when I did my teacher training many of the papers and textbooks that were recommended reading were from Canada. I assumed that because Canadians had become used to accomodating French and English speaking paople they had become more accepting of other cultures, specifically the Native ones. Would that be a correct assumption on my part?

    ReplyDelete
  12. Terry, I've been to Whangerei, or at least driven through, on the way to the Cape Brett Track, I think it was. Not sure, it was a long time ago.

    You might have guessed from some of my posts that I think you can introduce intuitive math concepts from music, both through pitch and rhythm. Math is innate across humanity. I also had a physics professor who was very good at using natural phenomena such as waves, interference of waves, water turbulence, echo, rock skipping, etc. to teach scientific concepts and math. It's all around you there. You can teach those kids without spending all your time drilling them in a classroom.

    I know 'Once Were Warriors' was quite a violent movie and perhaps projected a too violent image of the Maori. I view it more as a universal film, not one specifically about the Maori.

    Don't burden yourself with trying to create a blog. If you want, you can write something and maybe email some photos. My email is marniedunsmore@gmail.com. It's on the contact info at the top right of the blog. Don't worry about it though. Only if you find the time. And no hurry. I'm taking a break from the blog for a week or so.

    Regarding the Canadian books you are using, I'd have to have a look at the books to know what concepts and methods they're using. There is a terrible history in Canada regarding the schooling of native children in residential schools. Starting in the sixties, in part because of that terrible history, focus was put on a better system.

    Residential school system:
    http://www.cbc.ca/news/canada/story/2008/05/16/f-faqs-residential-schools.html

    By the time I was in elementary school in the seventies, enough progressive school teachers were changing the system. Some of the books I read in elementary school were books about the wild, which somehow captivated me:

    Lost in the Barrens
    http://en.wikipedia.org/wiki/Lost_in_the_Barrens

    The Bears and I
    http://books.google.com/books/about/The_bears_and_I.html?id=KYEaAAAAMAAJ

    I Heard the Owl Call my name
    http://en.wikipedia.org/wiki/I_Heard_the_Owl_Call_My_Name

    Regarding official bilingualism, thank Trudeau. He's still a controversial figure, especially since by the end of his long tenure in government, the country had accumulated a huge debt which Canada spent the next 25 years paying off. However, his vision for a bilingual, multi ethnic society shines as a beacon for the world. A short synopsis of his thinking is encapsulated in the book "The Essential Trudeau" by Trudeau and Ron Graham.

    There's still a long way to go to bring good teaching to native communities in Canada. I was visiting some friends on Vancouver Island two years ago. The people I was visiting mentioned that they have their kids in public school there and they did tell me that the relationship between the native and non-native community is not good. In fact, at times, it is quite hostile and the hostility (overt and covert) is two way. The situation is not helped by the fact that the economy on Vancouver has taken a nosedive in the last then years or so.

    All the best, Terry.

    I'm taking a break from the blog until the middle of next week.

    Warmest wishes and happy holidays.

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  13. Terry, one final suggestion is the Exploratorium exibit on Polynesian Navigation. It's linked in the sidebar under ONLINE EXIBITS. Just in case you don't see it, here is the link:

    http://www.exploratorium.edu/neverlost/

    Another amazing teaching tool is the exibit on EVIDENCE:

    http://www.exploratorium.edu/evidence/

    ReplyDelete
  14. In regards to a admixture in Europeans with a Northern Asian/Mesolithic population, check out:

    1. This wonderful blog, and it's 22 component admixture analysis and MAPS: http://magnusducatus.blogspot.com/2012/09/the-component-maps-of-mdlp-world22.html

    - note the Amerindian map, with a small concentration in West Central India - which as I commented, may be the root of Y-DNA P

    2. Check out this video of a "Sean-Nos" (trans. Old Style) singer from the West of Ireland. Many people might mistakenly think he has Native American ancestry, look at the strong nose, wide face and high cheekbones. There's your Mesolithic right there at 0:15 seconds:

    http://www.youtube.com/watch?v=vGPUO1yEE7Y&list=FL0SuRXN3aqFO0VezEseM8mQ&index=4

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  15. Hi Paul,

    Distribution maps are interesting and may be suggestive of migration routes. As I've mentioned above in this thread, the high mobility of many First Nations in the Americas would make the strict usage of genetic distribution maps problematic.

    And regarding the use of faces, we all do it, of course. I've been looking at First Nations faces and people with Scots and Irish faces all my life. We could discuss, but it would probably be a pretty long discussion, without any conclusive picture.

    I'm reading the early accounts of La Verendrye and Radisson. Also rereading some stuff on Tecumseh. The impressions of these early explorers of the people they encountered are very curious.

    ReplyDelete
  16. "I've been to Whangerei, or at least driven through, on the way to the Cape Brett Track, I think it was".

    That sounds right.

    "Distribution maps are interesting and may be suggestive of migration routes. As I've mentioned above in this thread, the high mobility of many First Nations in the Americas would make the strict usage of genetic distribution maps problematic".

    But as they moved around those groups would have spread their genes and so maps of the distribtion would be very revealing. It may even be possible to work out the pattern of those movements by examining the haplogroups at a fine definition.

    "Don't burden yourself with trying to create a blog. If you want, you can write something and maybe email some photos".

    I have made some maps of the distribution of mt-DNAs in SE Asia. I might scan them and send them to you, to do with tham as you wish. The maps are related to an entry that Luis has set up, specifically the 'west to east' and 'east to west' maps:

    http://ourorigins.wikia.com/wiki/Human_Prehistory_and_Genetics_Wiki

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    Replies
    1. "But as they moved around those groups would have spread their genes and so maps of the distribtion would be very revealing."

      Maybe. What concerns me is that there are at least three possible routes into the Americas. And it looks there were multiple migrations along each of these three routes at different times. Then on top of this, most of these groups were highly mobile.

      It does look like there is a detectable migration down the Pacific Coast that swung right down, through the Channel Islands of California, then around, and up into the Gulf of Mexico . . . That's a clearly defined coastal path.

      However, once you get to migrations through the rivers and lakes, there are multiple intersecting paths: Lake George, the Hudson, the Great Lakes, Lake Winnipeg, Riviere Rouge, the Missouri, the Mississippi, the Saskatchewan, the Bow, the Kootenay, the Athabaska, the Peace, the Columbia, the Fraser, the Sacramento, the Colorado . . .

      No simple paths discernable.

      "I have made some maps of the distribution of mt-DNAs in SE Asia."

      Terry, I am not sure that you know that most First Nations groups are just coming around to the idea of their genetic relationship to Eurasia. Many groups still do not want to have their DNA tested.

      There is this conference coming up October and I'm curious to see what indigenous Americans have to say about all this. So, for now, I'm going to hold off on looking at distribution maps.

      Delete
    2. This comment has been removed by the author.

      Delete
  17. Terry and Luis,

    The Haldane's sieve blog just put up this paper/software announcement for EasyGWAS.

    http://arxiv.org/abs/1212.4788

    I think Luis mentioned recently that those huge ADMIXTURE runs were killing his computer. EasyGWAS might be an improvement.

    ReplyDelete
  18. "there are at least three possible routes into the Americas. And it looks there were multiple migrations along each of these three routes at different times".

    I agree. The idea that there was just one migration into America has never made sense to me.

    "It does look like there is a detectable migration down the Pacific Coast that swung right down, through the Channel Islands of California, then around, and up into the Gulf of Mexico . . . That's a clearly defined coastal path".

    And to me that looks like mt-DNA B. B has not been found in Eurasia north of japan, which implies its route to America was by sea from Japan. American B is B2 and that is part of B4b. B4b1 has been found in Hainan and the nearby South China mainland and B4b1a reaches into the southwest Pacific as far as the Admiralty Islands. To me that's indicative of a coastal expansion around the Pacific.

    "There is this conference coming up October and I'm curious to see what indigenous Americans have to say about all this. So, for now, I'm going to hold off on looking at distribution maps".

    Are you aware of any regional concentration of the various clades within the American haplogroups A2, B2, C1, D1 and X2a? Their relationship with Eurasian haplogroups is easily seen in Phylotree, in case you're not aware of the tree:

    http://www.phylotree.org/tree/main.htm

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  19. "Are you aware of any regional concentration of the various clades within the American haplogroups A2, B2, C1, D1 and X2a?"

    I am not aware of regional concentrations of these haplogroups. I don't follow the topic that closely. In any case, here's a short list of papers, some recent, some not so recent, on the topic:

    Ancient and Modern Genetic Variation in the Americas:
    http://public.wsu.edu/~bmkemp/publications/pubs/Kemp%20and%20Schurr%202010.pdf

    California Prehistory: Colonization, Culture and Complexity:
    http://books.google.com/books?hl=en&lr=&id=fFX066QfQv8C&oi=fnd&pg=PA291&dq=chumash+haplogroup&ots=nhTGR2Z_rM&sig=N3Uu9V6fpY52e_FYscNs2j6trs4#v=onepage&q=chumash%20haplogroup&f=false

    Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas:
    http://onlinelibrary.wiley.com/doi/10.1002/ajpa.20543/abstract

    Rapid coastal spread of First Americans: Novel insights from South America's Southern Cone mitochondrial genomes
    http://genome.cshlp.org/content/22/5/811.short


    Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups
    http://www.cell.com/current-biology/retrieve/pii/S0960982208016187

    ReplyDelete
  20. Radisson's diaries, and Agnes Christina Laut's book "Pathfinders of the West" are important documents in that they describe Radisson's early contact with the Cree, Hurons, Iroquois, Ojibwe, Algonquins, Assiniboines, Sioux and Mandans.

    http://books.google.com/books/about/Pathfinders_of_the_West.html?id=M6vbPAAACAAJ

    ReplyDelete
  21. Free download site for "Pathfinders of the West":

    http://www.ebooktakeaway.com/pathfinders_of_the_west_agnes_c_agnes_christina_laut

    Downloads are at the bottom of the page.

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  22. Those links are pretty much the sort of thing I was looking for. From 'Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups':

    "Haplogroup D4h3 spread into the Americas along the Pacific coast, whereas X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets".

    That alone is very intertesting. And from 'Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas':

    "here named D1g and D1j, within the pan-American haplogroup D1. They both show overall rare occurrences but local high frequencies, and are essentially restricted to populations from the Southern Cone of South America (Chile and Argentina)".

    To me that suggests they were amoung the first arrivals in America. They moved furthest, although Luis would possibly claim they moved all the way south after the rest of the continent was already inhabited.

    And this is the most interesting link of all:

    http://public.wsu.edu/~bmkemp/publications/pubs/Kemp%20and%20Schurr%202010.pdf

    "The view that some population in Asia today will resemble the proto–Native American population is not plausible, as it ignores the fact that populations on the other side of the Bering Strait have undergone an equal degree of genetic evolution since their separation".

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    Replies
    1. Hi Terry, yes, the Kemp/Schurr chapter is a summary of work done to date on the Americas. It's very detailed.

      I possibly agree to your other comments as well, but I haven't had a chance to thoroughly read through all the material. It is a vaste topic, as complex as the prehistory of Europe.

      Delete
  23. wiki pages for First Nations groups encountered by Radisson:

    Iroquoian:
    http://en.wikipedia.org/wiki/Wyandot_people
    http://en.wikipedia.org/wiki/Erie_people
    http://en.wikipedia.org/wiki/Iroquois

    Algonquian:
    http://en.wikipedia.org/wiki/Cree
    http://en.wikipedia.org/wiki/Algonquian_peoples

    Siouan language group:
    http://en.wikipedia.org/wiki/Mandan
    http://en.wikipedia.org/wiki/Assiniboine_people
    http://en.wikipedia.org/wiki/Sioux

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  24. Another important paper on the peopling of the Americas:

    Beringian Standstill and the Spread of Native American Founders:

    Tamm et al.

    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000829

    ReplyDelete

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