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 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.

Ancient DNA from two 11,500 year old burials in Alaska

Today I and my collaborators have a new paper published in PNAS!  Justin Tackney, the lead author of the paper, was kind enough to write up a summary of the findings to publish here on Violent Metaphors. Here is his take:

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The Lost City that isn’t.



“La Ciudad Blanca” (“the White City”) is a legendary “lost” city, deep in the rain forests of the Mosquitia region of eastern Honduras. Charles Lindbergh reportedly spotted it from the air in one of his excursions and explorer Theodore Morde supposedly found the “City of the Monkey God,” which some have speculated to be Ciudad Blanca, in the same approximate region in 1939. However, Morde died without passing on the location of his supposed find, so his story was not verified. Nevertheless, interest in the legend of Ciudad Blanca has remained high among the public and the popular media. Numerous subsequent expeditions have gone in search of this lost city, all to no avail.

But according to Douglas Preston (yes, THAT Douglas Preston) in an article for National Geographic published in March, the legend of Ciudad Blanca has been vindicated and the “lost city” is lost no more.

“An expedition to Honduras has emerged from the jungle with dramatic news of the discovery of a mysterious culture’s lost city, never before explored. The team was led to the remote, uninhabited region by long-standing rumors that it was the site of a storied ’White City,’ also referred to in legend as the ‘City of the Monkey God.’”


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Republicans aren’t anti-vaccine. (Yet)

Last night’s G.O.P debate was notable for many reasons, but it was a particular low point for anyone concerned about public science literacy.  It’s becoming increasingly evident that the G.O.P. candidates are being duped by a false narrative of political polarization on the issue of vaccine safety.  And that is alarming.

This  is a better illustration of what vaccination is really about. Courtesy of Microsoft stock images, so it's even free!
What vaccination is really about. Courtesy of Microsoft stock images.

The CNN moderator for the debate last night asked Dr. Ben Carson, a neurosurgeon, to respond to Donald Trump’s often repeated assertion of a link between vaccines and autism. That link is a lie, but neither Dr. Carson nor Dr. Rand Paul (an ophthalmologist) called it out as such. Dr. Carson vaguely (but correctly) stated “There has — there have been numerous studies, and they have not demonstrated that there is any correlation between vaccinations and autism,” and “Vaccines are very important,” but then he qualified this by saying “Certain ones. The ones that would prevent death or crippling. There are others, there are a multitude of vaccines which probably don’t fit in that category, and there should be some discretion in those cases,” and “You know, a lot of this is — is — is pushed by big government.” Dr. Paul didn’t do much better, saying “I’m all for vaccines, but I’m also for freedom.”

(Source for transcribed quotes)

Let’s be perfectly clear: None of the objections Trump raised to vaccines have the slightest basis in biology, medicine, or reality. None. Not one. Nor does the “too many too soon” argument that Dr. Carson floated. As Tara Haelle put it:

“The problem is, our country doesn’t make or recommend vaccines that aren’t important, that don’t prevent death. So, I have a question for Dr. Carson. Below are the vaccines recommended through age 18. I’d like to know which one of these we should “use discretion” with. Which ones are not important enough to administer?”

You can check out the list and the rest of her article here.

Trump will be Trump, but we deserve more from the two physicians in this race. To be honest, I believe that both of them understand and accept the science on vaccines, but they’re pandering to what they believe Republican voters want to hear. But study after study has shown that vaccines are not a partisan issue–the same proportions of conservatives and liberals both accept that they are safe, sound, and necessary to combat infectious disease. Carson and Paul are completely out of touch with conservatives on this issue, and unfortunately their assumption about what their base wants to hear on this issue may itself change those numbers. Colin McRoberts discussed the potential consequences of turning this into a partisan issue a few months ago:

“Right now, most people support vaccination and reject anti-vaccine talking points. (I know that can seem implausible, given how visible those hoary anti-science stories are online. But vaccination rates don’t lie—the vast majority of parents reject anti-vax scaremongering.) If we start drawing party lines on top of the vaccine debate, people will start to use their party affiliation to define their position on vaccines. They won’t realize they’re doing it. They’ll honestly think they’re making decisions about vaccines based on the facts. But they’ll be judging those facts based on the community they belong to, the way we all do. So we can’t let those communities be defined as anti-vax communities!”

Amy Davidson, writing for The New Yorker, nicely articulated the dangers of having presidential candidates giving legitimacy to dangerously unscientific positions:

“A lot of what Trump says—diplomacy by yelling, for example—would be dangerous if put into practice. But most of it, assuming he doesn’t actually get elected, won’t be put into practice. The refusal to inoculate children, though, is something that his admirers can try at home. No other candidate was willing to anger the ideologues by standing up for something as suspicious as science.”

We have seen the consequences of not vaccinating children earlier this year. Do we really want more outbreaks of preventable disease to threaten our communities?  The use of vaccines to protect the health of our children is not a Democratic issue or a Republican issue. It’s not a liberal or conservative issue. It’s simply what the best science available overwhelmingly supports. I urge conservatives in the Republican party to make this point to your representatives. Only the base can hold the leadership to account, and this is one issue where we all need to take a united stand.

Deep (Conspira)Sea Fishing: A Fundraising Drive

A large, diverse conference of people with very unusual beliefs is coming up. I want to attend as research for my book and blog posts on Violent Metaphors. Tickets are expensive, so we’re trying to keep costs down with a little crowdfunding. Please visit to donate if you can. If you can’t donate, just sharing the link is incredibly helpful. Pitch in, and let’s lay the groundwork for a deep discussion of far-out ideas next year! The following post is our original crowdfunding appeal.

Do you believe in acupuncture, alien abductions, ancient aliens, chi, crop circles, entity possession, “forbidden archaeology” or “forbidden religion,” homeopathy, near-death experiences, occult Nazi super-weapons, Planet X, poisoned vaccines, spiritual channeling, the new world order, or illegal immigrants from Zeta Reticuli? Do you go to bed worrying about the New World Order, the Vatican, the FBI, the CIA, the NSA, NASA, the WHO, the CDC, the UN, space aliens and/or demons conspiring against you and all right-thinking people? And are you convinced that the world is ruled from the Bohemian Grove, a secret bunker under the Denver airport, Bilderberg meetings, the Council on Foreign Relations, Buckingham Palace, alien worlds or other dimensions?

Probably not, or at least probably not all of it. But thousands of people do believe those things, and other things stranger than you can imagine. This January, dozens of experts these fields will gather together on a cruise ship called the Ruby Princess. It’s called, honestly and cleverly enough, the Conspira-Sea Cruise. They’ll spend seven days explaining, discussing, and even demonstrating their beliefs. Some of them are fairly famous, like Andy Wakefield and Sherri Tenpenny, who will be sharing their theories on vaccines. Others are relatively obscure, like Laura Magdalene Eisenhower, great-granddaughter of the former president, who claims to have been recruited for a secret Mars colonization effort and that stargates began opening around the Earth in 2012. For a full week, conspiracy theorists, dreamers, and snake-oil salesmen of every stripe will be preaching and peddling their wares.
I want to be there. You can help make that happen by visiting our Go Fund Me site We’re nearly halfway there!

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Open access and pseudoarchaeology: an encouraging update!


Back in July I wrote about a new collection of reviews of pseudoarchaeology books by archaeologists that appeared in the journal American Antiquity. I was delighted about this effort by the authors and editors–I think we need more of this sort of direct engagement–but very disappointed that the reviews were inaccessible to the majority of interested, non-academic readers. I and others called on the SAA to make this collection free for public access.

As it happens, a few weeks ago they did just that! You are now able to access the reviews through this link. (I would have written about this much sooner, but I’ve been swamped with work in my new position). In addition, I want to call your attention to the great perspective piece that Kristina Kilgrove wrote for Forbes, in which she nicely summarized the problem archaeologists have with the pseudoscientific approach to archaeology:

Archaeologists are trained as anthropologists to recognize and celebrate the diversity of humanity, both today and in the past. Eric Cline succinctly explains this in his review, noting “pseudoarchaeologists cannot accept the fact that the mere humans might have come up with great innovations such as the domestication of plants and animals or built great architectural masterpieces such as the Sphinx all on their own; rather, they frequently seek or invoke divine, or even alien, assistance to explain how these came to be.”

Kudos to the SAA for making this resource available to everyone, and many thanks to the archaeologists who took the time to write these excellent reviews, with particular credit to Don Holly for organizing them! I hope that more archaeologists and biological anthropologists will follow this example. (In this spirit, I’ve just submitted the final draft of a paper on mitochondrial haplogroup X that addresses many of the common misconceptions about it–see comments on this piece for examples– to an academic journal. I’ll update you guys when it comes out).

Mixed messages during National Immunization Awareness Month

Be a vaccine superhero this month !
Be a vaccine superhero this month !

I haven’t had the chance to write much here about vaccines recently, so I was delighted to participate in MHA@GW’s initiative to highlight vaccination for National Immunization Awareness Month with a series of posts from guest bloggers entitled “Why Immunize?” My post focused on science literacy, and how to communicate with others about this issue:

In all likelihood, parents have already made up their mind as to whether or not they’ll vaccinate themselves and their children. And in all likelihood, that decision was to vaccinate.

These parents are motivated by a shared concern for their children and community. They know that vaccines prevent many childhood diseases, and that by maintaining high vaccination rates in their community, they maintain herd immunity. Perhaps they’ve seen the comparison External link of morbidity rates in the pre- and post-vaccine era and understand the significant impact vaccines have made in preventing the worst childhood diseases. They may have been worried about the outbreak of measles among families who took their children to Disneyland earlier this year, which hit unvaccinated people the hardest External link. Regardless of how they came to this decision, the vast majority of parents understand External link that the risks of vaccines are low relative to their tremendous benefits.

This is good news for the health of our communities. It’s critical that we continue to talk about immunization, because vaccine opponents are relentless — see the comments on my piece External link here for many examples of the bad science and provocative rhetoric they employ.

Speaking up is the most important step, letting parents know that their decision to vaccinate is the safest and most common way people protect their children. The anti-vaccine minority is disproportionately loud, partly because vaccines are so safe, effective and ubiquitous that they become part of the background landscape of parenting. Fortunately, in reaction to harmful pseudoscientific scaremongering and events like the Disneyland outbreak, people are motivated to speak out in favor of vaccines.

You can read the rest of my post here.

But I was dismayed to see that just hours after my piece was posted, a mainstream news site posted an article purporting to give balanced coverage on “the vaccine debate”, but instead propagated the same old mistruths and pseudoscience that have been thoroughly debunked by the scientific community again and again. This article, which features comments from a “Montana mother” given the same weight as those from a trained physician, and concludes by telling parents how to get vaccine exemptions for their children before school starts, is utterly reprehensible journalism. It’s a depressing reminder that we can’t ever let up on our efforts to educate journalists, as well as the general public, on basic scientific and medical issues

So in honor of National Immunization Awareness Month, I’m asking all of you to make a small but meaningful contribution to this effort. Please share at least one example of good news coverage on vaccines with your online and in-person friends. Your voice makes a difference in this conversation.

h/t Tara Haelle for the link to the news article.

Good science communication means never calling them “retard” – even if you’re Nassim Taleb

Communicating science to people who aren’t scientists is very hard to do well. Nassim Taleb should be very good at it, based on his enormous book sales and even more enormous opinion of his own skills. But we all have our demons, and Taleb has succumbed to his. Rather than encouraging a healthy discussion about science, he’s picked a side and declared all-out war on the people who disagree with him. Taleb even admits that his strategy is to prevent conversations from happening by abusing and insulting people who question him, and encouraging his followers to join in. What’s the point of that strategy? It doesn’t help communicate science, resolve legitimate questions about the facts, or even address the supposedly evil motives of his critics. All it really does is feel good. Nassim Taleb has chosen self-gratification over real engagement. Let’s talk about why that’s unproductive and unethical.

Anger Controls Him by Jessica Flavin

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Public outreach that’s inaccessible to the public.


Edit 9/3/15: The SAA has opened up this collection for public access! See my post on it here. 

I was delighted to read at Jason Colavito’s excellent blog that the journal American Antiquity has just published a special section in its current issue that’s devoted to debunking popular pseudo-archaeological ideas.   This is a fantastic example of the kind of outreach that I (and many others) would like to see academics and academic institutions engage in.  I want to commend American Antiquity (and its parent organization, the Society for American Archaeology) for this.  But with a caveat: outreach actually needs to, well, reach its intended audience. Right now, that’s not the case.  Continue reading

Encouraging science journalism: The genome of Kennewick Man.

A little over a year ago the complete genome sequence of a Clovis individual, the 12,500 Anzick child, was published. His sequence gave us a fascinating glimpse of ancient Native American genetic diversity, and new insights into the early peopling of the Americas. At the time, however,  I was unhappy about how the media covered it:

“Unfortunately, several press reports chose to find controversy in a decidedly non-controversial story by giving undue weight to problematic “alternative” explanations of Native American origins, including the Solutrean hypothesis, and other “European contributions” to Native American ancestry.”

Last week saw the announcement (also from Eske Willerslev’s lab group: they’re amazingly prolific) of the sequencing of yet another significant ancient American genome: the 8,500 year old skeleton from Washington popularly called “Kennewick Man.”  This time the press did an exemplary job of covering the news.

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