Responses to some questions about our recently published paper on haplogroup X and North American prehistory

Just a few days ago, my co-author Deborah Bolnick and I published a paper in the journal PaleoAmerica on the subject of haplogroup X and Native American population history. Rather than writing a blog summary of it (which has been my usual approach for publications), we decided to try something different: make the paper itself open access and respond here to a few questions about it that we’ve seen from a variety of sources.  We hope that this approach will be helpful to interested readers!

What is the paper about?

We reviewed existing genetic data to answer the question: Could mitochondrial haplogroup X2a have been brought to the Americas by an ancient trans-Atlantic migration? This is a rather old question from the perspective of anthropological geneticists, but we’ve seen it appear in both academic publications and documentaries rather frequently. We thought it was worth revisiting in light of recent genetic publications.

Quite simply, we found that mitochondrial and genomic data do not support this migration hypothesis as the most plausible explanation for X2a’s presence in North America. Instead, the most parsimonious interpretation of the genetic data continues to be that haplogroup X2a had the same migration history and ancestry as the other founder Native American mitochondrial lineages (i.e., from Siberia). Based on the current evidence, we feel that there is no need to invoke a distinct origin for individuals bearing this lineage.

If’ you’d like another summary of the paper, Andy White wrote a very good blog post about it here.

Where can I get a copy?

We’ve sent a request to the publisher to make the paper open-access, and are waiting for them to process the request. We’ll update this post with a link as soon as the process is finalized. In the meantime, you can email us for a copy or find it on Jennifer Raff’s academia.edu page

How can you say that this proves once and for all that all Native Americans have exclusively Beringian ancestry when you haven’t sequenced all of them? Isn’t that unscientific?

We don’t say that. This work presents our best interpretation of all the genetic evidence currently available that are relevant to this question. In fact, we end the paper saying:

It is of course possible that genetic evidence of an ancient trans-Atlantic migration event simply has not been found yet. Should credible evidence of direct gene flow from an ancient Solutrean (or Middle Eastern) population be found within ancient Native American genomes, it would require the field to reassess the “Beringian only” model of prehistoric Native American migration. However, no such evidence has been found, and the Beringian migration model remains the best interpretation of the genetic, archaeological, and paleoclimate data to date.

We don’t think it’s likely that new evidence will suddenly crop up showing another source of ancestry for Native Americans, but it remains a formal, albeit remote, possibility. Should such evidence be found, it will require us to reexamine our models. But we can’t incorporate hypothetical results into our interpretations. That would be unscientific.

Doesn’t skeletal data contradict the Beringian hypothesis? What about the very early Paleoindians whose skulls look physically different from later and contemporary Native Americans? Aren’t they proof that Native Americans have European ancestry?

The skeletal data show changes over time in the cranial morphology of ancient Native American populations. It’s true that comparisons of skull shapes were, for a very long time, how anthropologists studied genetic relationships between populations. However, over the last few decades, we’ve developed the technology to assess biological relationships between individuals and populations by comparing genomes. It’s generally acknowledged that this is a more precise, direct means of assessing ancestry than morphology, which can be influenced by environmental, developmental, and cultural factors.

Furthermore, the genomes of several of the Paleoindians with differently shaped crania have been examined, and they show no evidence of different ancestry than later or contemporary Native Americans. For example, Kennewick Man, who we discuss in the paper, exhibited what some have described as “Caucasoid” cranial features. However, his overall genetic affinities group him with Siberians/East Asians, not Europeans. And his mitochondrial haplogroup is the most basal lineage of X2a so far observed. This result shows that X2a—and this Paleoindian cranial morphology—are compatible with Siberian ancestry.

Why the skulls of the earliest inhabitants of the Americas look different from the later indigenous inhabitants is a very interesting question. We suspect it has to do with evolutionary forces like selection or drift acting on morphology over millennia. Current genomic research just doesn’t show evidence that they had different ancestry from later Native American groups.

Isn’t it pretty well proven that Clovis technologies are descended from Solutrean technologies?

No. The majority of archaeologists think that the similarities between the Clovis and Solutrean points are either spurious or coincidental. Very, very few archaeologists interpret the data as supporting the Solutrean hypothesis. We don’t see the genetic evidence as supporting the Solutrean hypothesis either.

Archaeologists were wrong about the “Clovis First” hypothesis, so doesn’t that mean that you’re wrong too?

Why? These are two separate models. The model of Beringian genetic ancestry of Native Americans is not dependent on the Clovis First hypothesis; in fact, the same evidence from which the “Beringian Pause” model was developed—early coalescence dates of mitochondrial lineages and ancient DNA data—was an important component in overturning the Clovis First model.

In science, any hypothesis is falsifiable, and any model is provisional pending contradictory data. The overturning of the Clovis First model is a great example of the process working as it should.

Isn’t it unfair to critique the Solutrean hypothesis before it’s been fully “fleshed out?” There’s bound to be more data supporting it soon!

Any hypothesis is open to testing, otherwise it’s not scientific. And there’s no “waiting period” to protect a hypothesis until it’s gathered enough data to make it immune to criticism. This argument is a species of special pleading—no other idea in archaeology is treated this way.

What about the signal of “West Eurasian” ancestry seen in Native American genomes? Does it support a trans-Atlantic migration?

This finding has led to a lot of confusion among non-geneticists, and we address it in some detail in the paper. To summarize: Raghavan et al. (2014) and Rasmussen et al. (2014) studied the genomes of the Siberian Mal’ta individual and the Anzick-1 individual, respectively, and they found that a portion of their ancestry (between 14-38%) was derived from a population that also contributed alleles to the contemporary inhabitants of West Eurasia. Notably, the contemporary European gene pool appears to have emerged quite recently—within the last 8,000 years—as a result of significant migration and admixture events. We don’t know what the genomes of Solutrean peoples looked like, since none have been sequenced yet, but from these findings we predict that they would more closely resemble pre-Neolithic hunter-gatherers than contemporary Europeans [see Allentoft et al. 2015, Haak et al. 2015, and Lazaridis et al. 2014]. Importantly, based on the pre-Neolithic genomes that have been studied, it appears that these early European hunter-gatherers did not exhibit close genetic affinities to Native Americans.

Several studies have also formally tested the evolutionary relationships between Native American genomes and genomes from ancient and contemporary populations worldwide (see Rasmussen et al. 2015, Raghavan et al. 2015, and Lazardis et al. 2014). These studies have consistently showed that the model which best fits the current genetic data did not match the predictions of the Solutrean hypothesis. We discussed this in the paper, noting that the most supported model:

was one in which the population ancestral to Native Americans was derived from ancient North Eurasian and East Asian sources, while contemporary Europeans were derived from ancient North Eurasian and West Eurasian sources. In other words, gene flow was from the ancestral North Eurasian population into both the ancestral Native American and ancestral European populations. Lazaridis et al. (2014) did not find any evidence of Pleistocene gene flow directly from West Eurasians into Native Americans. Their model is also consistent with other studies, which have shown that 62-86% of Native American ancestry derives from East Asia.

We’ll update this FAQ with the answers to more questions as they arise, so do check back. If you  have any questions, feel free to leave them in the comments section and we’ll try to get to them as soon as our schedules allow.

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23 thoughts on “Responses to some questions about our recently published paper on haplogroup X and North American prehistory

  1. lesraff November 11, 2015 / 9:37 am

    Jennifer–As one Raff to another, glad you used your blog to summarize an article I am sure I would never get to see. It gives me a taste for how anthropological (is that a word) research compares to the medical research I see and make use of on a regular basis in the diagnosis and treatment of prostate cancer.

    Also wanted to alert you to a change in location of our blog :”Downsize, Maybe!” It is now part of ChicagoNow. Checkout the current post, because sometimes you have to just relax and smile.

    All non-Raff’s are welcome to read along as well.

    http://www.chicagonow.com/downsize-maybe/2015/11/first-doctors-without-borders-now-pathologists-without-houses/

  2. Deny Dudzik November 11, 2015 / 2:39 pm

    Thanks Jennifer. I followed your explanation and analysis and I’m not a geneticist. My daughter Beatrix Dudzik just received her PhD with Richard Jantz at UT Knoxville and I’m working my way through Kennewick Man. Fascinating stuff!

    Sent from my iPad

    >

    • Jennifer Raff November 16, 2015 / 7:44 am

      Nice! Best wishes to her. Is she postdoc’ing somewhere?

  3. Stuart Fiedel November 12, 2015 / 6:27 pm

    Jennifer,

    I must note yet again that the supposed demise of the Clovis-first model is based almost entirely on the bizarre and unique site of Monte Verde. Even if it is a genuine human occupation site (which I strongly doubt) it is followed by a gap of 1300 years with no archaeological traces, after which we have firm evidence at 12,900 cal BP of the rapid and ubiquitous spread of Clovis-descended fishtail point makers throughout South America. So any genetic input of hypothetical Monte Verdeans would have been minimal.

    With respect to your work on the Alaskan infants’ DNA, check out the new piece by A Gomez–Carballa et al. on the genome of an Inca sacrificial mummy. Its mtDNA type is a new sub-clade of C1b. They date the origin of C1b at 18,300 BP, much older than the TMRCA calculated from the Alaskan infant.

    On X2a: I think you are correct to dismiss the Solutrean migration theory. However, let me play devil’s advocate here. 1) We have very few Upper Paleo genetic samples from Europe. The ca. 35-50 k yr-old specimens from Russia and Romania seem to represent populations that went extinct. There are no Solutrean-associated samples. And cranial analyses suggest there is a discontinuity between the Upper Paleo and Mesolithic populations of Europe, therefore, the many Mesolithic samples are irrelevant. So we don’t really know what genomes were prevalent in western Europe at 25k BP. 2) There could have been Solutreans in the Mid-Atlantic region, but they might have died out completely or been swamped genetically by later arrivals (i.e., Clovis). This is no more or less improbable than the supposed pre-Clovis occupation of South America that you accept without reservation.

    SF

    • Jennifer Raff November 16, 2015 / 7:44 am

      Hi Stuart, please note that our genetic models do not depend on Monte Verde. Our model is based on the totality of data, including (a) our sense of how most archaeologists view Monte Verde, (b) genetic evidence from Paisley Caves that indicates people were present there in pre-Clovis times, and (c) molecular clock dating approaches that suggest people began dispersing throughout the Americas in pre-Clovis times. And, as we said at the end of our article, we will of course re-evaluate this model if robust genomic evidence supporting the Solutrean hypothesis is discovered — but that we cannot base our current scientific models on hypotheticals. I understand you disagree, but in our view Monte Verde is more than a hypothetical, given the archaeological evidence that has been presented and that many archaeological experts find convincing.

      • Stuart Fiedel November 16, 2015 / 9:41 pm

        Jennifer,

        The large difference in estimated TMRCA of C1b based on the Inca mummy genome vs. the USR infant’s mtDNA should illustrate the uncertainty and subjectivity of mutation rate analyses. I also suggest you look closely again at this study, published in Science in 2013:

        Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males versus Females
        G. David Poznik,1,2 Brenna M. Henn,3,4 Muh-Ching Yee,3 Elzbieta Sliwerska,5 Ghia M. Euskirchen,3 Alice A. Lin,6 Michael Snyder,3 Lluis Quintana-Murci,7,8 Jeffrey M. Kidd,3,5 Peter A. Underhill,3 and Carlos D. Bustamante3,*

        They explicitly calibrate both global Y chromosome and mtDNA mutation rates based on a Native American presence at Monte Verde at 14,600 cal BP. And this is not the first such study to do so.

        The Paisley Caves feces may not be human. See work by Paul Goldberg and colleagues on the sterols.

        If you think I am the lone crank still expressing doubts about MV, check out this talk by MacArthur “genius” and South American specialist Anna Roosevelt (go to 1:17):

        SF

  4. Stuart Fiedel November 19, 2015 / 7:08 pm

    postscript:

    Dillehay et al. are now claiming (in PLOSOne) a human presence at MV at 18,000, maybe 25,000 cal BP or even earlier. Any thoughts on how these new dates can be reconciled with the genetic data? (but note that any competent archaeologist would regard about 80% of the stuff illustrated as non-artifacts, and the reported contexts are, again, bizarre [small pits in a braided stream bed]).

  5. daviddiamondblog December 15, 2015 / 7:52 pm

    its bizarre how many flaws i find with this analysis but then you already knew about these flaws. first of all;

    my main point;

    the genomes start of the same. diverge from isolation. and then converge from re-integration. so if u were able to do actual accurate DNA tests you would of found that the older back you went the genomes would of had MORE in common not LESS.

    the population size was smaller a long time ago so less variation in genetic makeup and people would of been very similar.

    the gene you are looking for is present in both groups. but your population size is too small to detect it. in your sampling. and too long ago. a small number have it but the group is small. so it could be a large percentage.

    the population sizes back then rule out transmigration. a huge boat load of migrants would re-integrate the genomes quickly. so they already had the gene but not all of them.

    as the population increases from a very small sample size genetic variation takes place. but very slowly. the total number of people with gene increases but now the percentage of people with the gene decreases.

    through your studies you detect that none had the gene a really long time ago. well of course. because so few people were around you would have to be really lucky. it is undetectable.

    you then suppose the gene was introduced somewhere between then and now. and you know the other carriers are trans-Atlantic so you believe them to be the source. as the gene is now detectable because the population size has increased. it was always there but now detectable.

    your two groups have been isolated for so long that they are genetically variant so that indicates that no trans-Atlantic crossing was made.as they would be more similiar otherwise.

    again this is not logic. a trans-Atlantic migration at this point is not going to have a significant impact on the genetic make up of the group. unless a huge population migrated. at which point we would know about it somehow. there would be a record. ships. different tools and iconography etc. so that didn’t happen.

    how is it you are able to get accurate enough DNA samples from seriously old bones? we can’t do that very well in murder trials yet? again supporting my theory

    to summarize. they already had the gene in their genome. in small total numbers, but a reasonable percentage. making it hard to detect ages ago. as the total population increased the total number with the gene increased but percentage got lower. this would make it seem like it was introduced at that time. this is because its a sudden detection of the gene. but the source of introduction of the gene would have to be so great a migration to start having effects now.

    the gene was always present because the two groups started off not in isolation. then separated.

    thank you.

    David Diamond

  6. daviddiamondblog December 15, 2015 / 8:04 pm

    so once again. they already had the gene. but u didn’t detect because its within the margin of error.

    after a large period of time the gene becomes detectable in the population. the percentage is smaller so you conclude it is a recent introduction. from migrants.

    in actual fact it was already present but has been slowly getting smaller percentage wise but large total number wise. i.e. 20% to 80% like 2 : 8, then like 1000:10000 i.e. 10% to 90%

    it would be possible for migrants to cause a significant detectable change in the genepool quickly unless there was a huge migration. which would be detectable

  7. John C January 16, 2016 / 5:51 pm

    Thank you for making this information freely available.

  8. Jason March 12, 2017 / 12:12 am

    Hello Jennifer. Where can I get the mtDNA information for the hundreds of Adena skeletons from over 17 mounds that your partner D. A. Bolnick has been acquiring since around 2002 but never published?

    • Jason March 12, 2017 / 12:24 am

      Lisa Mills’ study of Hopewell mtDNA is well known. But what about the results of the equally important Adena DNA tests? Surely with over 193 skeletons sampled from 17 or more sites a glimpse into the mtDNA of at least one Adena community is possible.

    • Jennifer Raff March 12, 2017 / 8:08 am

      She may have published other data elsewhere, but I haven’t followed the literature on this closely in recent years. A google scholar search should turn up these publications. If you can’t access something, contact me and I’m happy to send it to you.

      • Jason March 12, 2017 / 10:08 am

        Hey J. Thank you for the prompt response. I have the paper on the Hopewell DNA. I was trying to find the data mentioned in this abstract for a presentation she did at the 78th Annual Meeting of the American Association of Physical Anthropologists:

        Anthropologists often assume that
        archaeological sites with similar
        cultural remains represent a single
        biological population, but cultural
        exchange can occur independently
        of gene flow. In this study, we
        evaluate how well this assumption
        applies to Adena sites (2500-1750
        ybp) in the Ohio Valley. These
        sites are characterized by
        accretional burial mounds, circular
        ceremonial earthworks, and
        distinctive artifacts, but the
        biological composition of the
        populations who created them is
        unknown. Some anthropologists
        hypothesize a single widespread
        population connected via gene
        flow, whereas others suggest that
        Adena communities were more
        independent, with each burial
        mound being used by a single,
        genetically isolated population.
        To test these hypotheses, we
        extracted DNA from the skeletal
        remains of 193 individuals,
        representing 17 Adena burial
        mounds in Kentucky.
        Mitochondrial DNA (mtDNA)
        haplogroups were assigned based
        on restriction fragment length
        polymorphisms and a 9-bp deletion.
        The first hypervariable segment
        (HVS I) was also sequenced in a
        subset of samples to determine
        mtDNA haplotypes and confirm
        haplogroup assignments. When
        considered altogether, Adena
        haplogroup frequencies were
        similar to those observed in other
        ancient and extant Native
        Americans from eastern North
        America. However, both
        haplogroup frequency distributions
        and haplotype networks indicated
        substantial variation among Adena
        burial mounds. These data provide
        some evidence of gene flow
        between sites, but genetic drift also
        played an important role in
        structuring the pattern of Adena
        mtDNA variation.
        Regularities of growth patterns in

  9. Jason March 12, 2017 / 10:09 am

    As for the 2002 reference–her tests on the Wright and Robbins Mounds DNA is mentioned in Mills’ study of the Hopewell Farm DNA from 2003 as having been from 2002….

  10. Melanie Deatrich May 8, 2017 / 6:37 pm

    What boggles my mind is the idea that this group of X2 individuals supposedly migrated along the same path as all the other groups over Beringia without leaving a trail of their DNA. How does that happen? How can we explain that there isn’t Haplogroup X DNA all over Siberia & additionally a more profound addition of X to the other Native American types if it happened like this?

  11. Jason August 16, 2017 / 7:31 am

    Bolnick has tested around 200 Adena skeletons from at least 17 sites in Kentucky. While the Hopewell mtDNA tests receive much attention (which they should) the Adena studies are at least of equal importance, since Adena was the precursor and contemporary of Hopewell (ca. 500 B.C.–300 A.D.) in the Ohio Valley. Adena sites have also been found in the Tennessee River Valley, New York State, Canada, and the East Coast (Delmarva Peninsula). There has been disagreement since the early 1900s on whether or not Adena and Hopewell were the same people. Genetic anthropologists who have studied the mtDNA of Red Ocher, Glacial Kame, Hopewell,
    and Mississippian peoples have stated for years that Adena mtDNA would go a long way to clarifying some of the picture of North American prehistory. These results need to be made available.

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