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Angela
02-04-16, 16:26
Reich and Haak are in on this one.

"Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

See:
http://advances.sciencemag.org/content/2/4/e1501385.full

"The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages."

So, the precipitous decline in overall population resulted in extinction of many mtDna lines, even though some survived.

I found this interesting about the various migration waves:
"Genetic studies of Native American populations are complicated by the demographic collapse and presumed major loss of genetic diversity following European colonization at the end of the 15th century (7 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-7)). However, geographically widespread signals of low diversity and shared ancestry (8 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-8)–13 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-13))—particularly striking in maternally inherited mitochondrial and paternally inherited Y-chromosome sequence data—suggest that small founding groups possibly initially entered the Americas in a single migration event that gave rise to most of the ancestry of Native Americans today (9 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-9), 12 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-12), 14 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-14)). In contrast, the distribution of some of the rare founding mitochondrial haplogroups (D4h3a along the Pacific coast of North and South America, and X2a in northwestern North America) suggests that distinct migrations along the coastal route and the ice-free corridor occurred within less than 2000 years (15 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-15)). Recent studies have identified a weak Australasian genomic signature in several Native American groups from the Amazon, compatible with two founding migrations (16 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-16)), although the Australasian gene flow may have occurred after the initial peopling (17 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-17)). Irrespective of the number of migration waves, the founding population appears to have rapidly grown and expanded southward (8 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-8), 14 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-14), 18 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-18)), with low levels of gene flow between areas following initial dispersion (12 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-12), 14 (http://advances.sciencemag.org/content/2/4/e1501385.full#ref-14))."

"The estimated times to most recent common ancestor (TMRCA) for haplogroups A2, B2, C1, D1, and D4h3a were highly synchronous (Fig. 3 (http://advances.sciencemag.org/content/2/4/e1501385.full#F3) and fig. S8), confirming previous interpretations that all five haplogroups were part of one initial population."

Whether they're right about the timing I don't know.

I was very interested to see if they said anything else about mtDna X2a, which they maintain may have arrived in the last 2000 years, but I couldn't find anything. With whom and from what direction did it come?

ThirdTerm
02-04-16, 22:10
Phylogeographic analyses at the highest level of molecular resolution (69 entire mitochondrial genomes) reveal that two almost concomitant paths of migration from Beringia led to the Paleo-Indian dispersal approximately 15–17 kya. 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. The examination of an additional 276 entire mtDNA sequences provides similar entry times for all common Native American haplogroups, thus indicating at least a dual origin for Paleo-Indians.


I looked up the citation (Perego et al. 2009) about the origin of mtDNA haplogroup X2a. This 2009 paper does not state that X2a arrived in the last 2,000 years and it dated that X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets approximately 15–17 kya. Perhaps Llamas et al. (2016) did not read the 2009 paper correctly, which actually concludes: "The initial Pleistocene migrations into the Americas may have occurred within a narrow time window of no more than 2000 years, with a succession of temporally distinct movements along the coastal route and the ice-free corridor."



How can the different geographical distributions of haplogroups D4h3a and X2a be explained? A priori, we can envision two possible scenarios. First, haplogroup X2a could have entered into the Americas by following the Pacific coastal path just like D4h3a and the pan-American haplogroups. However, in contrast to the other mtDNA haplogroups, it would have disappeared from the wave front of the expanding population at a very early stage, thus remaining confined to some coastal enclave from where it expanded exclusively toward the east after the complete retreat of the Cordilleran ice sheet. This scenario appears rather unlikely, given that it would require the disappearance of a lineage from the front of an expansion wave involved in the colonization of a previously unpopulated territory, a demographic situation in which the loss of lineages due to genetic drift is minimized [37].

Alternatively, haplogroup X2a might have arrived from Beringia through a path that was different from that followed by the pan-American haplogroups. According to environmental and paleoecological data, such a path existed and was represented by the ice-free corridor between the Laurentide and Cordilleran ice sheets, which opened approximately 15 kya [5] or possibly was never completely closed [38]. Through such a corridor, where some glacial-refuge areas have been recently identified [39], X2a could have moved from Beringia directly into the North American regions located east of the Rocky Mountains. This latter scenario would imply that the X2a expansion in America occurred in the Great Plains region, where the terminal part of the glacial corridor ended, and is in complete agreement with both the extent of diversity and distribution of X2a observed in modern Native American populations.

Angela
02-04-16, 22:27
I looked up the citation (Perego et al. 2009) about the origin of mtDNA haplogroup X2a. This 2009 paper does not state that X2a arrived in the last 2,000 years and it dated that X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets approximately 15–17 kya. Perhaps Llamas et al. (2016) did not read the 2009 paper correctly, which actually concludes: "The initial Pleistocene migrations into the Americas may have occurred within a narrow time window of no more than 2000 years, with a succession of temporally distinct movements along the coastal route and the ice-free corridor."

Thanks for checking on that, Third Term. It was my mistake; I misinterpreted what this paper was saying.

Yetos
02-04-16, 22:41
@ Angela

Solutrean Hypothesis?
always acts like a 'fairy tale' in my heart and in my mind!!!!!

Angela
03-04-16, 22:26
@ Angela

Solutrean Hypothesis?
always acts like a 'fairy tale' in my heart and in my mind!!!!!

I don't think so, Yetos. It looks as if the people bearing it came along an ice free corridor from Asia and arrived somewhere around the Great Plains. That we find it in tribes the Europeans encountered around the Great Lakes and even further east doesn't contradict that theory because some of those tribes are known to have originated along the Plains and only moved east later.

" However, X2a is a major mtDNA subclade in North America; among the Algonquian peoples (https://en.wikipedia.org/wiki/Algonquian_peoples), it comprises up to 25% of mtDNA types.[61] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-61)[62] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-mma-62) It is also present in lower percentages to the west and south of this area — among the Sioux (https://en.wikipedia.org/wiki/Sioux) (15%), the Nuu-chah-nulth (https://en.wikipedia.org/wiki/Nuu-chah-nulth_people) (11%–13%), the Navajo (https://en.wikipedia.org/wiki/Navajo_people) (7%), and the Yakama (https://en.wikipedia.org/wiki/Yakama) (5%).[63] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-Fagundes-63) Haplogroup X is more strongly present in the Near East (https://en.wikipedia.org/wiki/Near_East), the Caucasus (https://en.wikipedia.org/wiki/Caucasus_%28geographic_region%29), and Mediterranean Europe (https://en.wikipedia.org/wiki/Mediterranean_Europe).[63] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-Fagundes-63) The predominant theory for sub-haplogroup X2a's appearance in North America is migration along with A, B, C, and D mtDNA groups, from a source in the Altai Mountains (https://en.wikipedia.org/wiki/Altai_Mountains) of central Asia.[64] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-Meltzer200909-64)[65] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-Cambridge-65)[66] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-haplox-66)[67] (https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#cite_note-67)"

https://en.wikipedia.org/wiki/Genetic_history_of_indigenous_peoples_of_the_Ameri cas#mtDNA

Also, "This relative absence of haplogroup X2 in Asia is one of the major factors used to support the Solutrean hypothesis (https://en.wikipedia.org/wiki/Solutrean_hypothesis). However, the New World (https://en.wikipedia.org/wiki/New_World) haplogroup X2a is as different from any of the Old World (https://en.wikipedia.org/wiki/Old_World) X2b, X2c, X2d, X2e, and X2f lineages as they are from each other, indicating an early origin "likely at the very beginning of their expansion and spread from the Near East".[14] (https://en.wikipedia.org/wiki/Haplogroup_X_%28mtDNA%29#cite_note-haplox-14)"
https://en.wikipedia.org/wiki/Haplogroup_X_%28mtDNA%29#North_America

It's tempting to think that the difference in appearance of the Plains and Algonquin Indians has something to do with this difference in mtDna frequencies, but that's pure speculation, and as is the case with a lot of groups, it's mostly down to adaptation and drift.

Angela
03-04-16, 22:46
Razib Khan has a blog post up on the paper. This is the link:

http://www.unz.com/gnxp/early-and-rapid-settlement-of-the-new-world/?utm_source=rss&utm_medium=rss&utm_campaign=early-and-rapid-settlement-of-the-new-world&utm_source=twitterfeed&utm_medium=twitter