American Indians

Sometimes people wonder why human genetics projects should bother to involve anthropologists.

From now on, this seems like a good example: "Rebuilding the genome of a hidden ethnicity".

CORRECTED: This article originally stated that the Taíno were extinct, which is incorrect. Nature apologizes for the offence caused, and has corrected the text to better explain the research project described.

The news article reports on a conference talk by Carlos Bustamante, who is working on the population genetics of the 1000 Genomes Project samples. The project includes whole-genome sequencing data from 70 research subjects from Puerto Rico, many of whom have a substantial fraction of ancestry from the native peoples of the Caribbean, chiefly Taíno. There are more than 4 million Puerto Ricans today, both on the island and throughout the United States, and their ancestry averages around 15% Native American. Genetically, that works out to 1.2 million copies of a typical gene derived from indigenous peoples, of course scattered in different ways across the genomes of Puerto Rican people today. That's a lot of information, and Bustamante and colleagues are using the information to test hypotheses about the ancestry and pattern of native ancestry in these people.

The news coverage of the talk ran into trouble by describing the Taíno as an "extinct ethnicity". What happened next won't be a surprise to any anthropologist who works in the Caribbean. Over the course of a weekend, the comment section of the Nature news article was filled by people outraged at the description of their ancestors as "extinct". Many identified themselves as Taíno people, protesting an injustice.

The communication failure here is obvious. A presentation that refers to descendants of an ancient population ought to use terms that are anthropologically valid. Here we have two words that provoked confusion and anger: "extinct" and "Taíno".

"Extinct" just is not a term that should apply to the ancestors of living people. Whatever the dictionary may say, to an ordinary reader or listener, the closest association of "extinct" is probably "dinosaurs". Extinction without issue. Even when we refer to cultural practices, the term "extinct" invites confusion. Extinction implies a model of disappearance that is sudden and complete, which in many cultural contexts didn't happen.

"Taíno" is a contested cultural category. A growing group of people today claim Taíno identity, not merely Taíno ancestry, who live on many Caribbean islands. Some cultural practices derived from pre-Columbian Taíno people are today still widespread, among people who may have no strong belief about their ancestors 500 years ago. The movement toward greater self-identification as Taíno has emerged within an international population. Any discussion of Taíno ancestry ought to be framed in terms of the living people today who have that ancestry. Some of them may have a small fraction of Taíno ancestry but still self-identify in that category; others have never self-identified in that way, a few of whom might even be horrified at the prospect.

Genetic observations themselves have contributed greatly to the revival of the concept of Taíno identity. By demonstrating the high fraction of indigenous ancestry in Caribbean people, genetics has provided something more "real" to people than their cultural ties may seem. Past studies of admixture in the Caribbean were hailed by activists as "scientific proof" that the Taíno still exist. That is one of the anthropological problems: the geneticists are not neutral players in this social milieu, even if they have no commitment to any possible result.

In my opinion, the 1000 Genomes Project participants are the good guys. The scientists directing the project have given a lot of thought to their selection of samples, funded workshops to discuss ethical issues that arise from sampling and analysis, and even came up with boilerplate language so that their hundreds of postdocs have a standard way refer to the different sample groups. The project has created tremendous value for those of us who study the range of human diversity and human origins.

Some of the project scientists have worked to explain why it is important to encompass human diversity within large-scale sequencing projects (for example, a recent paper by Bustamante and colleagues [1]). Genetic studies of human populations have been strongly biased toward European populations, and secondarily toward populations from other parts of the world that are well-represented by immigrant communities within the United States and Western Europe. The bias means that we don't understand as much as we should about the relationship between genetics and health in other populations of the world. Rare variations, some of which contributed to disease risk or protection, are missed by our current samples -- even though in some cases more samples could be added at minimal cost.

My point is that there are really good intentions behind the project, and from an NIH-centric perspective, the project attempted to be inclusive. But competing ideas of identity make human genetics a difficult area where miscommunication is inevitable. Categories that a human geneticist may think are perfectly clear, an anthropologist will tend to be more wary about.

I saw the story on Gene Expression, where Razib Khan provides good commentary along the lines of my reactions. I would add that cases like this one add a deeper dimension to the usual kind of science miscommunication. People are sometimes very selective about the science they accept to believe. Probably in no cases are people so selective as when the outcome concerns their own identity.

A great power of today's genetic technology is the opportunity it presents to allow people to discover their ancestry. But that power is easily twisted into a license to impose identity. When different groups have motives to construct genetic identity, then genetics becomes a powerful tool for each group to proselytize its particular version of cultural identity.

Anthropologists are already engaged in this problem, in different parts of the world. Yet they are minor players. As we see in this article, the geneticists have large voices. Those voices are heard rapidly by activists of various kinds, who have extremely high levels of engagement with broader communities. Taíno and Nature are both obscure to most Americans, but within 72 hours one of those groups mobilized and forced a response from the other, in a way that will have a large impact on future scientific and news reporting.

References

This is such an incredible story about the "Clovis comet" hypothesis, I don't know where to start: "Comet Theory Comes Crashing to Earth".

Oh, well how about we start with the fact that the idea's main exponent is living under an alias:

Indeed, the team’s established scientists are so wedded to the theory they have opted to ignore the fact their colleague “Allen West” isn’t exactly who he says he is.

West is Allen Whitt — who, in 2002, was fined by California and convicted for masquerading as a state-licensed geologist when he charged small-town officials fat fees for water studies. After completing probation in 2003 in San Bernardino County, he began work on the comet theory, legally adopting his new name in 2006 as he promoted it in a popular book. Only when questioned by this reporter last year did his co-authors learn his original identity and legal history. Since then, they have not disclosed it to the scientific community.

Well, the whole thing was thoroughly vetted by the National Academy member who coauthored the paper, right?

After the theory was first announced in 2007 in Acapulco, Mexico, [Vance] Holliday had attempted to collaborate with [NAS member James] Kennett to test the idea. But Kennett effectively blocked publication of the study last year after the results didn’t support the comet theory.

Err...well...you certainly can't dispute the physical evidence, right? I mean, what about the high concentration of carbon spherules that were associated with the supposed impact?

On March 25, Boslough reported that radio-carbon dating of a carbon spherule sample shows it is only about 200 years old — an “irregularity” that indicates is it not from the alleged 12,900-year-old impact time.

This means that a sample from a layer purporting to show a high concentration of spherules at the inception of the Younger Dryas actually only was about as old as the Declaration of Independence.

The article discusses whether the carbon spherules may have been deliberately "salted" into the samples by someone, presumably West/Whitt himself. The quote I pulled as the title of my post, "I would run screaming," comes from another geologist asked whether he would work with West on anything.

This story has really unraveled into a geological version of Piltdown. Like Piltdown, there were many people who were outright skeptics from the start -- because the evidence just didn't make sense. And like Piltdown, there are true believers who will not give up even after the physical evidence is shown to be questionable, possibly doctored.

Anyway, I've written about this several times:

"A hard bolide to swallow?"

"The Younger Dryas impact fizzle?"

You can tell when I really think an idea is nonsense: all the blog post titles end with a question mark!

I'm using some statistics out of William Boyd's 1956 printing of Genetics and the Races of Man[1]. It gives a good accounting of blood group data known more than fifty years ago, which I'm using to illustrate my intro lectures. Meanwhile, there are some interesting passages, from the standpoint of today's knowledge of the human genome and its variation.

On skin pigmentation -- this is the earliest statement I've run across of the argument that the New World pigmentation cline is shallower than the Old World cline because of the relative recency of occupation (pp. 178-180):

The aborigines of the New World, though not by any means identical, agree in having on the whole considerable skin pigmentation. If pigmentation is adaptive, and conforms to climate, why are not the Eskimo and the inhabitants of Tierra del Fuego as light as Europeans? This looks like a considerable difficulty, but the solution is probably comparatively simple. The aborigines of the New World have not been here for more than about 25,000 years, or about 1000 generations. They are by origin Asiatic, and in Asia skin pigmentation is fairly heavy. Unless the selection of light skin as opposed to dark were fairly intense, the time elapsed has simply not been enough to allow for much adaptation to occur (12). As a matter of fact, the populations which might have been expected to become lighter, namely the Fuegans and the Eskimo, have probably had a shorter time in which to achieve this end than other American aborigines, for it is reasonable to suppose that the Fuegians did not reach their present home until long after their northern neighbors were well installed. And all students of the Eskimo agree in recognizing them as probably the most recent (aside of course from the whites) arrivals in America. It could well be that there has just not been enough time for selection to bleach the skins of the American aborigines.

Reference 12 is Haddon's Races of Man, which I have requested from the library.

I'm following up, because skin pigmentation is one of the traits most clearly subject to recent rapid selection. The new mutations that lighten skin tone in Europe and Asia are only partially shared between those populations. Many alleles are very common in one population, but nearly absent in the other. So far, the estimates of dates for these new variants are all within the last 20,000 years, but many remain undated. So we can't specify the level of pigmentation of people 15,000-20,000 years ago, yet, but it would have been substantially darker than those populations today.

Which leaves us with the same question, but from the opposite perspective. We now know that pigmentation evolved rapidly in Eurasia, the strong gradient of pigmentation having increased greatly within the last 20,000 years. We also know that the occupation of temperate South America began quite early, with people having been there longer than 10,000 years. So why did the New World end up with a more gradual cline -- darker pigmentation in the temperate and Arctic regions, lighter in the tropics than in the Old World? Was selection less intense? Can we attribute the difference to demography? Or chance?

Boyd next alluded to a demographic explanation -- low population density:

In any case, the pre-Columbian population was so sparse compared with that of Asia and India that on a statistical basis alone we should be justified in asserting that skin pigmentation conforms to climate.

Them's some tricky statistics.

We would of course today recognize that the sheer number of people is not especially relevant; much more powerful is the independent occurrence of a similar response in two long-separated populations. But Boyd was concerned with a different issue: Some had been claiming pigmentation as a neutral trait, making it more useful as a race marker:

This has been denied chiefly by those who were concerned to prove skin color a non-adaptive character, so that it might safely be used in the classification of races (12). Since the more up-to-date students of anthropology have given up the idea of relying on non-adaptive characters, or even believing that any such exist (13), there is no longer much dispute about the probable adaptive value of skin color (emphasis added).

Well, makes me glad to be an "up-to-date" student! There in fact has been an ongoing debate about "non-adaptive characters" as concerns the relationship of Pleistocene people. Many geneticists were surprised to discover the persistence of Neandertal genes, but in fact the skeletons of Upper Paleolithic Europeans clearly bear Neandertal traits. The debate for the last 30 years hasn't been chiefly about the presence of these traits, but instead about whether they were adaptive. Some argued that adaptive traits were not suitable evidence for a relationship, because they could emerge by parallelism in distinct populations.

Others observed that adaptive traits were more likely to be shared among populations linked by gene flow.

Now, of course, we have remaining unanswered questions about these shared traits. The shared traits are clearest between Upper Paleolithic Europeans and European Neandertals. We don't have genetic information yet telling us about the extent of Neandertal gene sharing with these early Europeans. Was it more than elsewhere? The traits would argue for it.

What about the Neandertal genes in populations far from Europe? One might expect Neandertal-like morphology to show up at some low level. Of course morphological features are polygenic, so that phenotypic resemblance falls much faster than genic identity. And Holocene populations have continued to evolve. Maybe early Asian skeletal remains like the Upper Cave skulls (ca. 11,000-20,000 years old) actually reflect that Neandertal heritage to a greater extent than recent samples.

Then there is the likelihood of other contributions, more local ones, to later populations.

Returning to the topic of pigmentation, many of us used to assume that the light skin of Europeans in part reflects Neandertal ancestry. That is, just as Boyd suggested, it would have taken a lot longer than 25,000 years to get the current strong cline of skin pigmentation in the Old World. If you could have longer, getting lighter pigmentation from earlier inhabitants of Europe, for example, you could explain a stronger cline with the same strength of selection.

I no longer think this is necessary. It's still possible that we got some pigmentation variants from Neandertals, but we haven't found any yet. And we've been looking. It does seem that Neandertals had some of their own pigmentation variants. Maybe we'll find many more of those, maybe not.

References