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.

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.

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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New study overturns yet another anti-vaccine talking point

The pseudoscience community has long tried to convince parents that the MMR vaccine (to prevent infection with the diseases measles, mumps, and rubella) causes autism, despite study after study after study after study after study after study after study after study* showing that there is no connection between MMR and autism.

The pseudoscience community’s desperate investment in this myth–and the shaky ground they stand on– is illustrated by how quickly they shift their stories:

“Thimerosol or aluminum, or some kind of ‘toxin’ is the cause!”    Debunked .

“No, I mean, it’s just too many too soon!”    Debunked

“No, but seriously, natural infection is way better because unvaccinated children are healthier than vaccinated children!”   Debunked.

And just yesterday, another study  (Jain et al. 2015 Autism occurrence by MMR vaccination status among US children with older siblings with and without autism) has come out debunking yet another antivaccine myth: that the MMR vaccine somehow “triggers” autism in children who are genetically susceptible to it.

Time reveals the absence of integrity in pseudoscientific constructions.
Time reveals the absence of integrity in pseudoscientific constructions.

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Why the Food Babe is wrong (it’s not just because she’s ignorant)

You knew I had to talk about Food Babe this week.

My not-so-secret goal with this blog is to improve public science literacy and to help people become more critical consumers of information. As a consumer activist and critic with enormous influence, one might hope that Food Babe’s goals are similar to mine.  But I’m afraid I have to give her methods a big red F, and for distressing reasons. Before I get into that, however, I want to give readers who aren’t familiar with Food Babe some background.

Like the decision to vaccinate, the choices we make about food have significant consequences to our health.  It’s easy to find advice on how to structure our diet–there is an overwhelming volume of admonitions to eat more protein!, only organic!, less fat!, more fat!, plant-based!, paleo!, non-GMO!, raw!, Mediterranean!, gluten-free! with dire warnings about what will happen if we fail to follow that plan exactly. (I feel particularly sympathetic to parents of young children, who are already stressed out about the incredible day-to-day challenges of raising them in a difficult economy. Shaming them if they’re buying most of their food in bulk once or twice a month at Costco instead of shopping exclusively for their children at Whole Foods is outrageous.  In fact, the very ability to make choices about what we eat is a privilege not shared by a huge proportion of the planet’s population…but that’s a subject for another post).

For the average person untrained in science, nutrition, or medicine, the challenge of wading through this mountain of advice on how one “should” eat, sorting out the good advice from the bad, can be daunting.  With so many options it’s easy to succumb to decision fatigue–or default to way too many meals at fast food joints.

Diet and health gurus are counting on this. They offer people a simple solution: follow my “movement”, follow my advice and you don’t have to think for yourself about this; follow my simple “tricks” and you’re guaranteed “health”, “thinness” and a sense of belonging to a righteous movement.

Enter “Food Babe” (whose real name is Vani Hari).

Actions undertaken without understanding  are always foolish, and often dangerous.
Acting without understanding is always foolish, and often dangerous.

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New paper deals blow to hypothesis that Native Americans have European ancestry

The idea that Native Americans had at least some ancestry from a trans-Atlantic migration has been around since the earliest days of American anthropology. The earliest proponents of this idea looked at the spectacular burial mounds and art from North America and insisted that they could not have been made by the ancestors of the indigenous (or as they put it, “primitive”) peoples they encountered. Obviously, they reasoned, a “Lost Race” of “Moundbuilders” (identified variously as Atlanteans, Europeans, and Israelites) must have been responsible for the great archaeological sites in North America. But systematic excavation of these sites has thoroughly debunked that idea.**

Nevertheless, an idea that there must be a European origin for at least some Native Americans has persisted in various forms. In its modern iteration, this idea is known as the “Solutrean Hypothesis.” The Solutrean hypothesis claims that the Clovis people, the makers of the earliest known stone tools in the Americas, were the cultural and biological descendants of the Solutrean peoples of southwest coastal Europe.

I have written before about why the genetic diversity present in contemporary and ancient Native Americans does not support this hypothesis (“Problematic science journalism: Native American ancestry and the Solutrean hypothesis”). Here, I want to discuss a new challenge to the Solutrean hypothesis that came out in the archaeological literature just today.  Continue reading

Dear parents, let’s talk about measles

Vaccine superhero
Thanks to vaccines, L. is protecting other kids in her community. And by avoiding illnesses, she has more time for important stuff, like being a superhero. Photo by Colin McRoberts

Dear parents,

Livia, with permission of her mother
This is Livia. An unvaccinated child with measles potentially exposed her the disease, so she spent one of her first six months in quarantine. Photo courtesy of Jennifer Simon

You’re probably aware that measles has been in the news a lot lately. We need to talk about it again, even if you feel like it’s old news, because of Livia, Rhett, and Cami.
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The Good Fight Part 1: The Fine Art of Talking to People Who Are Wrong

The good fight is that special argument where you know you’re right, and just can’t imagine how anyone could possibly disagree. But they do, even when the disagreement is about something fundamental and irreconcilable. Did we evolve? Is the climate changing? Are vaccines safe? Do I really have to pay my taxes? The answers matter, but so do the arguments. Let’s try to improve them.

This is Part I in a series about how and why we have those difficult conversations, online and in the real world. We’ll explore ways to make them more persuasive, more fun, and more rewarding. For a practical example of where we’re going with this, see my earlier pieceThe Most Important Playground Conversation: How to Persuade a Friend to Vaccinate.  Going forward we’ll focus particularly on arguments with people who have irrational ideas, like anti-vaxers or creationists, but some topics apply in every conversation. This is one of them, because in every conversation you have to remember: you are talking to a person. They are as real, as smart, and as decent as you are. You’re having a conversation, not a battle. That’s the hardest thing to remember for all of us some of the time, and for some of us all of the time.

I was going to start this series by writing about goals and strategies, but then I got bogged down in a conversation on global warming that reminded me of that more fundamental rule. It doesn’t matter what your goal is if you let yourself forget that you’re talking to a real person. Personalizing an argument, making it about the people instead of the issues, poisons conversations. Once you start to think of the conversation as just another blunt object to apply to the other person’s head, you’ve already lost. So what happened, and what can we do about it?

"Alu finds a friend"

Not a friendly conversation.

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Storytelling vs. science

Things are not always what they seem.
Things are not always what they seem.

Several organizations exploit vulnerable parents by claiming that they can “cure” their children’s autism through various approaches.

As Left Brain, Right Brain observes, these “autism cure” movements persist because of the power of storytelling:

“Nothing sells unproven “treatments” like testimonials. For autism it has been true since the days of chelation and even before that. Tell people that your “treatment” cures autism and you have testimonials to show it and you can just about guarantee sales.”

As we all know, anecdotes aren’t scientific evidence, but they do appeal to us on an emotional level. Unfortunately, one woman’s recent experience has starkly illustrated just how untrustworthy such stories actually are.

Camile Saulnier (a pseudonym) was recently given a book by Kerri Rivera called “Healing the Symptoms known as Autism”, which prescribed a “Treatment” for curing autism:

“I began looking into the background of CD/MMS and I was extremely concerned to find that MMS (Sodium Chlorite + Citric Acid = Chlorine Dioxide) aka. ‘CD’ was and is being hailed and marketed as a cure for almost every ailment and disease known to mankind, this includes Cancer, Malaria, Aids and Ebola.

I found the man behind MMS to be one Jim Humble, the Arch-Bishop of a rather cult like church named the “Genesis II Church”. Suffice to say I was very worried indeed, I searched further and found that Kerri Rivera the author of the book “Healing the Symptoms known as Autism” is a Bishop within this church.

I voiced my concerns with my friend who was following the Protocol, but she seemed to be un-phased by my doubts. She directed me to the facebook group CDAutism, where she said I will find proof of the recovery stories and thousands of parents giving testimony to the marvelous gains achieved by using the CD Protocol.”

Saulnier was justifiably concerned and spent some time reading the group’s posts, learning that the linchpin of the group’s claims was the collection of testimonials of parents of “recovered” autistic children. Saulnier was skeptical about the reliability of these testimonials, as they were all posted by Kerri Rivera, and so devised a little test to see how Rivera determined what “recovery” was and whether it was the CD treatment that caused “recovery.”

“I had an idea to see for myself, I needed to be sure 100% that everything I was seeing and reading was real before I could even consider using this protocol. I am afraid my worst fears were not only imagined, they are real.

I made a recovery story for my child, based on so many others which I had read, I felt bad doing it as I do not like to pretend but it was for the sole purpose of finding a greater truth.”

Saulnier’s false testimonial was immediately and enthusiastically posted by Kerri Rivera on the group’s website, and the banner proclaiming the number of children “cured” of autism was promptly updated to reflect this false cure. You can read the details of Saulnier’s correspondance with Rivera here.

Now, I’m not at all comfortable with Saulnier’s approach. I don’t believe that it’s ethical to lie. But having said that, it is a fascinating glimpse into the credulity of this segment of the alt-med community. Can you imagine how this would have played out in the science-based medical community? What level of scrutiny would such a story have been subjected to by physicians and medical researchers before they accepted it as true?

Several readers of this blog are persons on the autism spectrum and have contributed their perspectives in discussions on vaccination and autism. I’d particularly love to hear their thoughts on this issue.