My research

Archaeological Fantasies and the genetic history of the Americas

Jennifer Raff14 Comments

The excellent podcast Archaeological Fantasies recently had me on as a guest for a wide ranging discussion on genetics. We covered everything from the genetic prehistory of the Americas to issues surrounding ancestry testing companies. Here’s a link to the episode (apologies for the fact that I kept cutting in and out–apparently our university wireless connection isn’t very good).

Since so much of our discussion focused on haplogroup X2a and models for ancient American prehistory, I decided to break from the normal tradition here at VM and actually re-publish a post to make it easier for people to get answers to any questions they might have. And if you have specific questions about content from the podcast, please feel free to leave them in the comments on this post.

This post was originally published last year to address some questions that Deborah Bolnick and I were getting about our paper “Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas? A Critical Re-Evaluation.”  I’ve edited it slightly to reflect the fact that the paper itself is now open access, and you should be able to download it here or at my academia.edu page. (I’m actually really shocked at the number of downloads it’s gotten…apparently this is a topic that a lot of people find interesting!).

As soon as my syllabi for the upcoming semester are finished, I will try to write up another post that summarizes recent findings in North American anthropological genetics, and what they mean for our understanding of the initial peopling of the Americas. In the meantime, if you’re interested in ancient DNA I highly recommend you get up to speed on some of the methods by reading this post.

 

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

Jennifer Raff10 Comments

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 Genetic Analysis of the Alaskan North Slope

Jennifer Raff7 Comments

My colleagues and I have just published a paper on the genetic diversity and population history of contemporary Iñupiat peoples (the indigenous inhabitants of the North Slope of Alaska) in the American Journal of Physical Anthropology.  It’s open-access for at least a few months, so you can read it in its entirety here, our collaborator Dr. Anne Jensen ‘s thoughts on it here, and Archaeology Magazine’s article on the paper here. I’ve also summarized our findings below.

Here I am working at the Nuvuk site in 2009.
Me, working at the Nuvuk site in 2009.

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

Jennifer Raff21 Comments

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 →

The genetic prehistory of the North American Arctic

Jennifer Raff2 Comments

I’ve been waiting for this paper for months! The Willerslev group has just published the results of their study on ancient DNA from Paleo-Eskimos in the North American Arctic. Unfortunately, this article is behind a paywall at the journal Science, but I’ll give you a brief summary of the results, and talk a bit about why this paper matters and what it means for our understanding of the peopling of the Americas. Continue reading →

Nicholas Wade’s troublesome approach to scientific critiques

Jennifer Raff197 Comments

Nicholas Wade has a problem. Although his new book, “A Troublesome Inheritance: Genes, Race and Human History”, appears to be selling well, he’s not encountering the praise that he expected from biologists for “courageously” freeing them from the “intimidating social scientists” on the subject of race).

Plus ça change, plus c'est la même chose
Plus ça change, plus c’est la même chose

 

 

What is he arguing? I go over this briefly in my recent piece on the Huffington Post, and in much greater detail here on this blog, but essentially Wade is using patterns of human variation in populations as a justification for claiming that race is a valid, biological taxonomic category. He goes on to speculate (and that’s really the only word for it, since his claims are unsupported by the preponderance of scientific evidence) that these racial differences determine behavioral differences and thereby explain why some civilizations have historically been more successful economically and politically than others. (You can guess which races he’s talking about; his speculation happens to coincide neatly with traditional stereotypes.)

Wade claims that all critics of this viewpoint are motivated by political concerns and ignore data showing that races are genetically distinct enough to be meaningful taxonomic categories of humans. His book relies particularly upon one genomics study to support this point. In his words (emphasis mine):

 

Raff and Marks take issue with one of these surveys, Rosenberg et al. 2002, which used a computer program to analyze the clusters of genetic variation. The program doesn’t know how many clusters there should be; it just groups its data into whatever target number of clusters it is given. When the assigned number of clusters is either greater or less than five, the results made no genetic or geographical sense. But when asked for five clusters, the program showed that everyone was assigned to their continent of origin. Raff and Marks seem to think that the preference for this result was wholly arbitrary and that any other number of clusters could have been favored just as logically. But the grouping of human genetic variation into five continent-based clusters is the most reasonable and is consistent with previous findings. As the senior author told me at the time, the Rosenberg study essentially confirmed the popular notion of race.

 

It’s not a question of logic, but rather what the data show. Rosenberg et al. (2002)’s paper did not analyze or identify just 5 clusters, but rather it considered 1-20 clusters. What Wade is omitting from his paragraph above (and also from his book) is that Rosenberg and colleagues never presented any statistical justification for the choice of 5 clusters over any other number.

Here are the specifics of my criticism, which I posted in response to a commenter on my blog. (If you’re not interested in the statistical refutation of Wade’s argument, feel free to skip this paragraph. I hope Wade takes the time to read it, though). Continue reading →

What an ancient Paleoindian girl tells us about Native American prehistory

Jennifer Raff17 Comments
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Photo by Paul Nicklen/National Geographic from http://www.nature.com/news/mexican-skeleton-gives-clue-to-american-ancestry-1.15226?WT.mc_id=TWT_NatureNews

 

 

More than 12,000 years ago, a young teenage girl walking through a deep cave (known today as Hoyo Negro) fell down a massive pit. The fall fractured her pelvis, and she died among the remains of giant ground sloths and saber-toothed cats who had met a similar fate. Over the next few millennia, the pit filled with water and their bones were covered with cave formations. They were left undisturbed until discovered in 2007 by cave divers, who named the girl “Naia” in a reference to Greek mythology.

Today, a team of archaeologists and geneticists announced the results from sequencing her mitochondrial genome. She possessed a haplogroup (D1) that evolved in Beringia and is seen in modern Native Americans.

So why is this result so important? The Hoyo Negro girl, like other Paleoindians (the oldest inhabitants of the Americas), had a skull shape that was distinctive from later (younger than 9,000 years before present) ancient Americans, who more closely resembled modern Native Americans. Continue reading →

Problematic science journalism: Native American ancestry and the Solutrean hypothesis

Jennifer Raff148 Comments

This is the second post in a series discussing the recent publication of a 12,500 year old genome from Montana. You can find the first post here.

In the weeks following the publication of the complete genome from a Clovis child, there’s been a lot of press coverage of this study and its possible implications. I want to discuss a bit of the media coverage on this subject, since it raises issues that I think science journalists need to consider more carefully.

First of all, to recap the major findings of the original study (discussed in more detail at the link above):
1. Anzick-1, the 12,500 year old Clovis child whose genome Rasmussen and colleagues sequenced, is very closely related to living and ancient Native Americans.
2. Anzick-1 is more closely related to Siberians than other Eurasian groups.
3. Anzick-1 is more closely related to Central and South American Native American groups than to some North American groups.
4. The results from Anzick-1’s genome fit with the scientific consensus about the peopling of the Americas. This consensus encompasses the results of decades of archaeological, genetic, and paleoclimate research.

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.

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Clovis tools from the Anzick site. From Rasmussen et al. 2014.

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The oldest North American genome and what it tells us about the peopling of the Americas

Jennifer Raff49 Comments

Last Wednesday, Dr. Morton Rasmussen of the Natural History Museum of Denmark and his colleagues announced that they had completely sequenced the genome of an infant boy, buried ~12,600 years ago in Montana. A few weeks earlier, I’d been approached by an editor at Nature, who asked me if I and my mentor Deborah Bolnick would be interested in writing a companion paper that would analyze and contextualize their results. We agreed, and the paper was published in last week’s issue, alongside Rasmussen et al.’s work. Because it’s (unfortunately) behind a paywall, I’d like to summarize what we said in that paper for non-scientists. There are a lot of things to talk about with regard to this study, including a consideration of ethical issues and the media’s response, so I’m likely going to do several posts on it. This first post is mainly a discussion of how we interpret the results.

For a TL;DR version of this post, here’s a link to a short interview I did on the subject last week with the BBC World Service.
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Nature publication

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I haven’t been writing as much here recently, because I’ve been working on a “News and Views” article for Nature….and now I can finally talk about it! Here’s a link to my article: http://www.nature.com/nature/journal/v506/n7487/full/506162a.html, and to the paper that it’s discussing: http://www.nature.com/nature/journal/v506/n7487/full/nature13025.html. In the next few days I’ll post something here to discuss the main points of the article (for those of you who can’t access it), and also my reaction to the media coverage that the study is getting.