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Haplogroup X2a and the Peopling of the Americas

11/7/2015

13 Comments

 
If you're interested in how, when, and from where people first entered the Americas, you should be aware of a new paper by Jennifer Raff and Deborah Bolnick titled "Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas? A Critical Re-Evaluation" (PaleoAmerica 1(4):297-304). It is a concise, clear, and largely non-technical essay discussing what the presence of mitochondrial Haplogroup X2a in Native Americans might be telling us about the pre-Columbian migration of populations across the Atlantic. 

The answer is . . . (drumroll): not much.
PictureMap showing geographical distribution of Haplogroup X among living populations (Wikimedia Commons).
Haplogroups are genetic populations that share a common ancestor.  The common ancestry of mitochondrial haplogroups is defined by differences and similarities in mitochondrial DNA, a kind of DNA that is contained in the mitochondria of cells.

Haplogroup X is found in living populations in Europe, west Asia, and northern North America.  Studies in the late 1990s began to ask whether the geographic distribution of Haplogroup X among living populations was telling us something about the origin of at least some New World peoples. A widely-read 1998 popular article titled "Genes May Link Ancient Eurasians, Native Americans" (Science 280(5363):520) helped popularize the idea that peoples from the Near East or Europe contibuted to Native American ancestry.  This idea was very popular among Mormons looking for evidence of a migration of Near Eastern peoples to the New World several thousand years ago (it is regarded with less enthusiasm now, especially after the publication of genetic data from Kennewick Man: see this blog post, for example).  

The distribution of Haplogroup X has also been proffered as evidence by proponents of the Solutrean Hypothesis (the idea that Paleolithic peoples from Europe migrated to eastern North America around 20,000 years ago). In a 2014 paper ("Solutrean Hypothesis: Genetics, the Mammoth in the Room," World Archaeology 46(5):752-774), Stephen Oppenheimer, Bruce Bradley, and Dennis Stanford argued that

"The mtDNA X2a evidence is more consistent with the Atlantic route and dates suggested by the Solutrean hypothesis and is more parsimonious than the assumption of a single Beringian entry, that assumes retrograde extinction of X in East Eurasia." (from the abstract)

Raff and Bolnick's essay strongly challenges that interpretation, concluding the following (page 301):

"We remain unconvinced by the arguments advanced thus far in favor of a trans-Atlantic migration prior to 1500 cal yr BP or so. As we have discussed, X2a has not been found anywhere in Eurasia, and phylogeography gives us no compelling reason to think it is more likely to come from Europe than from Siberia. Furthermore, analysis of the complete genome of Kennewick Man, who belongs to the most basal lineage of X2a yet identified, gives no indication of recent European ancestry and moves the location of the deepest branch of X2a to the West Coast, consistent with X2a belonging to the same ancestral population as the other founder mitochondrial haplogroups. Nor have any high-resolution studies of genome-wide data from Native American populations yielded any evidence of Pleistocene European ancestry or trans-Atlantic gene flow."

This is an interesting case where, I think, interpretations based initially solely on genetic information from living populations are and will continue to be refined as data are added from prehistoric remains.  Genetic data from living populations are great for formulating hypotheses, but they don't actually provide direct evidence about the past -- that has to come materials and skeletons that are actually from the past.  Whatever story is "true" has to be consistent with all lines of evidence.  Raff and Bolnick (page 301) mention that there are currently no genetic data from Solutrean skeletal material -- I hope someone pursues that in the near future.

As a final aside: it's a bummer that every single paper I discuss in this post is behind a paywall. I can get to them through my university library access, but the public generally can't.  A lot of people out there who are not professional academics are interested in these issues and it's a shame we can't make our work more openly available to them.  The Raff and Bolnick paper is a great example, I think, of an essay on a technical issue that is written in such a way as to be palatable to a non-technical audience (and when it comes to genetics, I include myself in that audience).  I hope that their paper can somehow be made open access so anyone and everyone can read it.​

Update (11/7/2015):  A copy of Raff and Bolnick's paper can be downloaded from Jennifer Raff's Academia.edu page.

13 Comments
Jennifer link
11/7/2015 05:34:42 am

Thanks for the nice write-up, Andy! Deborah and I have always intended this paper to be open access, and I'm currently working out payment details with the publisher. Hopefully it will be freely available for everyone soon. In the meantime, I've uploaded a pdf of it on my academia.edu page.

Reply
Andy White
11/7/2015 05:39:39 am

Thanks Jennifer - I've added a link in the post. Let me know if/when you get open access worked out and I'll add that information also.

Reply
Bill Hucks
11/7/2015 07:07:10 am

Just a genetic enthusiast here who previously believed the Solutrean Hypothesis! I have not read the article, but
it seems Kennewick Man has answered one of the most intriguing questions in human migration to the Americas. Hap X's disappearance in East Asia is a mystery that may never be solved. Could it be related to the 'third' unknown and mysterious Northern Eurasian contribution to the human genome?

Reply
Jennifer link
11/8/2015 05:41:03 pm

Hi Bill, I'd be happy to send you the article if you email me. jennifer (dot) raff (at) ku (dot) edu.

Reply
Bill Rouslin
8/14/2016 02:28:03 pm

Thomas Schroeder
8/16/2016 10:41:39 am

I regularly find my way back to your blog. This time, via an Ohio Archaeological Council post from Jennifer Raff. I had read this blog post before but today want to dig deeper.

"Raff and Bolnick's essay strongly challenges that interpretation, concluding the following (page 301)".

That scared me into thinking I needed to read hundreds of pages to get a rudimentary understanding. Luckily, the paper begins on page 297!

BTW, Steve Timmermans finally responded to you at length here:

http://www.andywhiteanthropology.com/blog/hey-popular-archaeology-here-are-some-corrections-to-your-solutrean-hypothesis-story

If you responded again, I would be interested in ready what you have to say. I have communicated with Steve and read his Southwinds site paper but still struggle to understand what, specifically, is seen in Paleo lithics that support an Alantic migration more so than a Pacific.

Reply
Andy WHite
8/16/2016 10:46:02 am

Hi Thomas,

I'm behind on responding to blog comments. I'm hoping to revisit a lot of the posts I've written re: peopling, Paleoindian, etc., after the semester settles in. There are a lot of things to talk about for sure.

Reply
Canuck
10/19/2016 11:24:56 am

Hi !
I just recently got a X2a result that surprised the heck out of this Irish-Canadian girl and I have been digging around on the internet to figure this out. I have a passing interest in DNA and phylogenetics, but know nothing about anthropology.

I see you mention the Solutrean hypothesis but not Anishnaabe oral history. When I saw the distribution of X2a, I saw a close overlap with Anishnaabe. A little digging brought me to the history of the Anishnaabeg, who came from the East (dawnland, between MicMacs and Abenakis - likely today's Nova Scotia, or maybe Newfoundland) and headed West starting in about 900, following a prophecy. They stopped in Montreal, Niagara Falls, Michilimackinac, then over to Sault Ste-Marie and west into Ruperts Land/Wisconsin, where they came to be known as Saulteux, Ojibwe, Chippewa. This oral history matches the distribution of X2a very well, and may help explain the East to West distribution pattern. Eastern names for the Anishnaabe include Algonquin, Mississauga, Odawa, Nipissing,

The Anishnaabe prophecy is an interesting read all on its own. It may reference first contact, from the North American point of view.

I am guessing you already know all this, but I couldn't find any quick references to First Nations histories on your blog so I thought I would mention it in case you are not familiar with the Anishnaabe stories.

Cheers!
PS, yes the DNA test was right - my mothers (all of them back as far as I could find) were born in Algonquin territory.

Reply
John Bierma
12/4/2016 06:10:24 am

Why is the halpo x found in the Windover site in Florida never factored into this debate? Who has tried to discredit that evidence?

Reply
Donna B
11/3/2017 06:28:11 pm

Tragically the DNA testing at Windover was horrible botched. They had a problem with contamination and in the end destroyed what little DNA they had left. Initial reports of what they found varied. The only final results they would give was that the DNA was Asian and X haplogroup was found.They did not say what subclade of X, which is major issue when discussing X2a or some other group. The time frame between the different X groups is significant.

Reply
Gabe walker
1/1/2017 10:31:21 pm

Kanaani looking for copper? It seems hard to ignore the map. Most x comes from levant where shipbuilding started and strong on the st. Lawrence to the Great Lakes. Occums razor seems like that right? My Canadian friends take sailboats down the mississip up the Atlantic and then either Hudson or st. Lawrence home. It's way easier than people realize.

Reply
noel
6/12/2018 03:33:05 pm

http://www.mormondialogue.org/topic/70663-the-dna-issue-again/

The Mormons are having a spirited discussion about Raffs paper. What are your thoughts? Evidence of Book of Mormon peoples disappear without a trace? any evidence of Israelites ever being in the Ameicas?

Reply
lee
5/31/2019 07:53:28 am

The migration of people carrying the X2 haplogroup into the America's is really an interesting topic. Oppenheimer and Rath have different opinions on this topic, obviously. Unfortunately, the data is thin on the ground for either an Eastern or Western path for this haplogroup. It is further complicated by the fact that we need to be concerned with X2a and X2g. Below is an except of an unpublished review of the topic: "The maternal lineages marked by X2 mtDNA haplogroups are rare and widely scattered in general populations and have no clear migration path that brought them into the Americas (Juhasz et al. 2016). Contemporary distribution and diversity indices all indicate that the basal X2 mtDNA haplogroup (X2+225) spread out of the Near East, probably from Southern Arabian Ice age refugia (Fernandes et al. 2012). The specific refugia may have ranged from the Gulf oasis (Fernandes et al. 2012) through the then mostly dry Red Sea Basin (Gandini et al. 2016). Older estimates of the age of the X2 haplogroups had placed its age as far back as 29,000 years ago (Reidla et al. 2003). However, in a seminal paper, Behar et al. (2012) reassessed all mtDNA haplogroups and refined the nomenclature and age estimates. The revised age range for the emergence for the basal X2 mtDNA haplogroup now falls between 16,593 to 21,874 years ago (Behar et al. 2012, Fernandes et al. 2012).. However, the migration route from the Near East and into the Americas is unclear and may conflict with this new age range.
In contemporary Native Americans, the maternal lineages of interest for this manuscript are the mtDNA haplogroups X2a and X2g that are found exclusively in the North America Native populations. Both haplogroups descend from the basal mtDNA X2-225 that diverged and formed multiple branches including X2a’j and X2g’l (X2-225+ reversion mutation G153A, van Oven and Kayser 2009) starting around 17,076 ± 3096 years ago (Behar et al. 2012). Populations with these two intermediate basal haplogroups further diverged with the establishment of the X2a, X2j, X2g and X2l maternal lineages (van Oven and Kayser 2009). X2j mtDNA has been found in the remains from an Egyptian oasis (Kujanova et al. 2009), contemporary populations of Iran (Reidla et al., 2003) and Saudi Arabia (Fregel et al. 2015). The X2l mtDNA has been found in an individual from Germany (Parson and Dur, 2007), Iran (Derenko et al. 2013) and in multiple individuals from Turkey (Behar et al. 2008). The X2l mtDNA found in Turkey was originally defined as X2g (Behar et al. 2008), but redefined as X2l (Behar et al. 2012) as it does not share the same defining mutations as X2g found in the Ojibwa (Perego et al. 2009). These data suggests that ancestral populations to Native Americans became geographically separated from Western Eurasian/Near Eastern X2-mtDNA haplogroups after the divergence of the basal X2-225 mtDNA haplogroup into X2a’j and X2g’l mtDNA haplogroups but before divergence into further branches of maternal descent (Fernandes et al. 2012; ~14-19,000 years ago).
Populations with the X2a and X2g mtDNA haplogroups geographically center on the Great Lakes (Brown et al. 1998). Native American mtDNA haplogroup X2 lineages are found in the Ojibwas of Manitoulin Island (Northern Ontario) with around 25% of the population having mtDNA haplogroups of X2a (Scozzari et al. 1997). X2a mtDNA haplogroups are also found in other NA populations at various frequencies including the Mikmaq, Jemez people of New Mexico and Yakima people in the Northwest (Malhi et al. 2003, Brown et al., 1998, Malhi et al. 2001). Further, the basal X2a haplotype demonstrated expansion with the autochthonous development of multiple daughter haplogroups of X2a (X2a1, X2a1a, X2a1b, X2a2) (Fernandes et al. 2012, Perego et al. 2009) at 7,883 ± 2606 years ago (Behar et al. 2012). The autochthonous development and density of additional daughter haplogroups of X2a1 strongly suggest serial founder effects followed by a period of isolation with limiting gene flow from other populations. Further, the geographical distribution and timing of coalescence favor east to west expansion for the X2a1 and X2a2 mtDNA haplotypes (Oppenheimer et al. 2014).
It is currently unclear from where and when X2 mtDNA haplogroups entered the Americas. Presuming that current models for timing based on other haplogroups is correct, one estimate of mtDNA haplogroup X2a entry into the Americas from Beringia through the ice free corridor would be around ~13,000 years ago (Perego et al. 2009, Fagundes et al. 2008, Hooshiar Kashani et al. 2012, Heintzman et al. 2016). If entry was near to the coalescence time for X2a, when it split from the basal X2 a’j mtDNA haplogroup, this could push entry back as far as ~16,225 years ago (Behar et al. 2012) and far before human colonization through the ice free corridor was probable (Heintzman et al. 2016, Pedersen et al. 2

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