The Yang paper and the reality of race

A new genetics paper by Yang et al published online in the journal “Human Genetics”, also commented on elsewhere, is of considerable interest. I would like to make a few comments about this paper. Groups tested were European-Americans, East Asians, Mexican Americans, Mexicans, South Asians, Amerindians, West Africans, African Americans and Puerto Ricans.

From the paper’s abstract, we read:-

Abstract
: We and others have identified several hundred ancestry informative markers (AIMs) with large allele frequency differences between different major ancestral groups. For this study, a panel of 199 widely distributed AIMs was used to examine a diverse set of 796 DNA samples including self-identified European Americans, West Africans, East Asians, Amerindians, African Americans, Mexicans, Mexican Americans, Puerto Ricans and South Asians. Analysis using a Bayesian clustering algorithm (STRUCTURE) showed grouping of individuals with similar ethnic identity without any identifier other than the AIMs genotyping and showed admixture proportions that clearly distinguished different individuals of mixed ancestry. Additional analyses showed that, for the majority of samples, the predicted ethnic identity corresponded with the self-identified ethnicity at high probability (P > 0.99). Overall, the study demonstrates that AIMs can provide a useful adjunct to forensic medicine, pharmacogenomics and disease studies in which major ancestry or ethnic affiliation might be linked to specific outcomes.

Of interest is the use of the term “ancestry informative markers” and the fact that Shriver’s buddy Rick Kittles is one of this paper’s authors. Is there a potential DNAPrint connection here? How similar or different is the methodology used in this paper to that of DNAPrint, of particular interest in that boosters of this paper include critics of DNAPrint?

Note that accurate ethnic identification was obtained without any prior information about the individuals sampled. In other words, a “blind” study of human genetic variation was able to correctly “bin” individuals into the correct racial categories (based upon their – after the fact – revealed ethnic self-identification and place of origin), and was able to determine “admixture proportions” that were able to identify mixed-race individuals. Very interesting, indeed, if “race does not exist”, eh? And to those who rant about “clinal variations” among human groups, and that Paabo has “proven” that human genetic variation is purely clinal and that clustering is merely some sort of artifact of ignoring admixed populations, I note the following from this paper:-

These findings and implications differ from those suggested by the recent studies of Serre and Paabo in which the microsatellite data set utilized by Rosenberg was reexamined (2004). These investigators suggested that observations of continental grouping in population structure analyses is due to the sampling methods and that there are gradients of human genetic diversity rather than discontinuities between the continents. In contrast, the current study using diallelic AIMs supports the conclusion that the continental population groups are relatively discrete and that such results are not due to limited sampling and exclusion of admixed populations. As discussed subsequently, the robust results observed in the current study may depend on the use of diallelic AIMs ... Although multi-allelic markers such as microsatellites may also be used for examination of population structure (Rosenberg et al. 2002), it is likely that these markers will show considerably more noise in the analysis due to the presence or absence of low frequency alleles and stutter polymorphisms. In addition, the higher mutation rate suggested for microsatellites as compared with SNPs may result in less correlation of such markers with ancestry. These differences may, in part, account for the robust results in the current study compared with those reported by Serre and Paabo (2004) using microsatellites. In addition, the number and geographic origin of the samples may account for differences between such studies.

Indeed. The current study specifically included admixed populations, yet clusters were readily observed. In addition, a simulated “Eurasian” group was able to correctly bin those self-identified “East Asians” (Filipinos, see below) who tested with some European genetic affiliation. This strongly suggests that the inclusion of groups like Central Asians would not in any way alter the ability to cluster racial groups; those peoples would be detected as were the admixed Filipinos.

The issue of these Filipinos brings up another crucial point – the “errors”, the “mismatches” detected were those that would be entirely expected from the known population histories of the ethnic groups considered. Therefore, they are not “errors” at all. For example, the Philippines were a long-time colony of Spain; the Spaniards intermixed with the natives there as they did in Latin America (albeit to a lesser extent). Indeed, to give a flavor of the small number of “anomalies”, I quote from the paper:-

The exceptions were: one of 72 Amerindians, and two of 80 East Asians that have a large contribution from the cluster that is predominant in the European American population (cluster 1 in Fig. 2), and one of 88 European Americans and one of 88 South Asians had a minor contribution from the cluster predominant in West Africans. Interestingly, the two East Asian subjects were both of Filipino origin (two of 28 Filipinos included in the self identified East Asian subject group) … However, the variability in best ethnic group assignment was mostly where the probabilities for an individual were similar between two related ethnic groups and most of the “miss-assignments” may reflect the “true” ethnic affiliation, e.g., for African Americans, a large number could not be distinguished from West Africans and for Mexicans, multiple individuals could not be distinguished from Amerindians.

Hmm … Filipinos with some European ancestry, Mexicans similar to Amerindians, African Americans that could not be distinguished from pure West Africans (some black Americans are relatively unmixed) – not surprising, is it? It would seem that, taking this into consideration, accuracy of identification was ~ 100%. And I thought “race is a social construct with no biological validity?”

Admixture proportions are what would be expected from history, other population genetics studies, as well as DNAPrint tests. African Americans are primarily West African, but with a substantial European minority component. Puerto Ricans have a substantial West African component and a minimal Amerindian component to go along with their European component. Mexicans are a European-Amerind mix. Interestingly, Mexican Americans had less Amerind ancestry than the Mexicans, which may be contrary to expectations. However, sampling may be a reason for this – the Mexican sample was from Mexico City; while, it is probable that the Mexican American sample was skewed in favor of the older, “legal” Mexican families, and away from more recent illegal immigrants and their progeny. I find it unlikely that illegals are volunteering for many genetics studies.

Of particular interest is the case of the South Asians. First, despite the fact that the authors were unable to find many markers that were characterized by large frequency differences comparing European-Americans and South Asians, the cumulative genetic differences were such that the South Asians were clearly separated from the European-derived peoples. Thus, contrary to comments like “South Asians are just dark-skinned whites” or “South Asians are just brown-skinned Europeans” (which even John Baker seemed to imply, at least about North Indians, in “Race”), we see that South Asians are clearly in a racial category separate from persons of European ancestry.

Some people have attempted to use the South Asian results to attack the DNAPrint tests; thus, we need to examine the facts to reveal the truth. When only four clusters (k = 4) was used in the analysis, South Asians appeared to be an admixture of European and East Asian populations. However, the authors state that:-

However, at k = 5 or greater, the STRUCTURE analysis shows the presence of a new cluster (here designated cluster 5) in the South Asian subjects (Fig. 2b, c). This cluster was the predominant group in the South Asian population for each of the South Asian subjects and was present in the other populations only in small percentages.

Er … this is actually consistent with the DNAPrint data, in its broad perspectives. The combined ABD and Euro data from DNAPrint showed that the predominant genetic component of South Asians was a characteristically “South Asian” genetic signature, and that this particular component was found at low levels in other groups (eg, Irish, Iberians, Italians, Turks, etc). The Yang study does indeed show low levels of East Asian and European genetic affiliation for South Asians even with k = 5, so the DNAPrint critics are perhaps being a bit disingenuous in their attacks. In summary, the Yang data for South Asians is reasonably consistent with DNAPrint, albeit with somewhat differing proportions.

Another interesting finding was the possibility of the detection of “substructure” in European-derived populations, as a minority cluster at k = 6. This was most pronounced in the European component in the Hispanic groups, prompting the authors to speculate:-

….whether this finding is due to a difference between southern European populations and northern European populations or possibly unique to Spanish populations. The latter might be explained by the Moorish or Arabian influence in this population.

Or perhaps Sephardic influence in the Spanish component? However, given the presence of this at lower levels in the European-American and African-American samples (and given the presumption that admixture in African Americans is mostly of NW European origin), I also speculate that this may be indicative of this Paleolithic/Neolithic European divide.

Finally, I note that the authors of this work make a subtle distinction between actual ancestry and comparative genetic components, similar to points I have been trying to make about the DNAPrint tests:-

It is less clear how accurately these STRUCTURE analyses reflect true ancestry….the AIMs are a limited set, i.e, they do not reflect true population diversity, their use in these analyses may be quite advantageous at least with respect to ascertainment of major ancestral components.

To project this to DNAPrint – what would be needed for accurate analysis of actual direct ancestry are more AIMs, more powerful algorithms, and – very important – more and more varied parental populations to determine the allele frequencies. And the authors of the Yang study seem to understand that the same limitations apply to their work. However, the data in both cases are perfectly sound in getting a solid view of the relative, comparative genetic (“ancestral”) components of different groups, and thus to “bin” individuals into different clusters of major groups, as well as the identification of admixture within groups and individuals.

In both cases – Yang and DNAPrint – “blind” studies of individuals correctly identify majority race with ~ 100% accuracy, as well as identify, in many cases, significant admixture consistent with known population histories and with individual phenotypes. The point being, in the last analysis, is that while a more perfect analysis would be able to detect “true ancestry” and complete “population diversity” (including Australian aboriginals, Papuans, etc.), the more limited set of AIMs and parental populations are currently sufficient to identify major racial and sub-racial populations, and admixture of these, by observing the patterns of genetic components characteristic of each group.

Thus, even if DNAPrint (or Yang et al) would label the different clusters as A,B,C, D and NOT with actual names of population groups, and even if we did not know the exact origin of these genetic components, we could say, for example, that North Europeans are characterized by, typically, a profile of proportions 6A, 2B, 1C, and 1D, while Southern Europeans were 3A, 4B, 2C, and 1D, and Middle Easterners were 0A, 1B, 6C, and 2D, etc.

In any case, in summary:-

Race is real. And South Asians are a different race than Europeans. And the results of the Yang paper are generally consistent with the broad outlines of the racial and sub-racial DNAPrint data.

Posted by JW Holliday on Monday, October 3, 2005 at 12:59 PM in Genetics & Human Bio-Diversity
Comments (12) | Tell a friend

Comments:

Posted by liberallarry on October 03, 2005, 02:51 PM | #

Race and ethnicity. Ethnicity and race.

It was Johanne who declared there were five races: white, malayan, mongolian american-indian, etheopian.

Take a man from England and compare him to a frenchman. Okay, subtle differences. Compare the frenchman to the German. Subtle differences. Now continue east through Poland, and Russia. Yes, differences. The man from Poland is much different from the man in England, but when you go from village-to-village from France to Moscow, you will see the slight variations. Branch to the Balkans, and notice the Slavic heritage, and how it blends with the indigineous people of Turkey. Continue through Turkey, and you can identify a difference between a Turk, and an Iraqi. In fact, there are a few different kinds of Iraqis based on their native villages. If you go east, to Iran, the arabs there will resemble Pakistanis moreso than Egyptians.

If you continue east, the differences in a Pakastani and Indian can be often confused unless your eye is trained for the differences. Carry on through the Punjab region, through Bangledesh, and notice how these natives resemble more of the Laosian, Viet breeds. Notice when you go further north, how there is a slight change between a Cantonese, and a Cambodian. Go further north, and notice the subtle differences between a Manchurian Chinese man, and a Cantonese Chinese man. Go further north, and see the people of the steppes, the Mongolians. Go further west into the steppes, and see the Turks, who, as you continue going west, will bleed into Arabia to the south, and slavs to the north.

Go northeast from the Mongolians, where the indigineous people of Kamchacta will resemble the natives of Alaska. An eskimo is white skinned compared to the chinese man, but resembles a chinese much more than a european in genetics.

The changes between Indian tribes is noticable between the northern-most part of America, to the southern-most part. The Indians of Sioux are noticably different then those of the Snohomish in Western Washington, or the Iroquois of New England, or the Apache and Pueblo Indians of Arizona.

In a way, there is no difference between race and ethnicity. It just depends on how broad of a definition you want to get into.

There is also a difference in other species across the world. Take the fox, and how it has adapted to its environment. The arctic Fox, the desert fox, the red fox, gray fox, and any in between and not included. Take a look at the different kinds of bears, and how they have adapted to meet their environmental needs.

Humans are the same. We’ve adapted in different ways as we spread in all directions across the planet. Tools were also developed based on need: The wheel was invented in the middle east, but also it shows up in Incan ruins. The rough terrain made its usage for carts impossible, but it did exist in Incan toys. Similarly, fire was harnessed in the north out of survival necessity. Meanwhile, the Polynesians who populate the myriad of islands in the Pacific got there by understanding buoyancy, and floating across the Pacific on logs.

So does race exist? Well, yes in a way. It depends on how much differences you want to look at. As you shrink to ethnic levels, do differences exist? Absolutely. Even the ethnic people of England can be dissected further. A welsh man will identify the different families quite easily.

It’s a wierd decision to decide what race ethnic groups are. They could be based on region quite easily, but there is a gray zone - An area of diffusion almost every time. Arabians and Russians are separated by the people of Georgia. So what are the people of Georgia, according to a European? Arab, Russian? Russian-Arab?? These differences can be overlooked real easily, creating future generalization and stereotyping that may not be realistic.

I would contend that race is an illusion. The article is very enlightening, but limited. An empirical research may seem to be impractical, though.

Posted by Svigor on October 03, 2005, 05:13 PM | #

I would contend that race is an illusion. The article is very enlightening, but limited. An empirical research may seem to be impractical, though.

Your entire post contradicts this assertion, unless you erect a strawman definition of race. Race is ethnicity, at least in the sense you’re using the word.

Your entire post comes down to semantics. Exchange the word “race” with whatever lovely new term you wish (ethnicity, population group, etc.,), my race-realism and tribalism changes not a whit.

Also, all clines are not created equal.

Posted by JW Holliday on October 03, 2005, 06:11 PM | #

You see, Larry, we’ve seen him before ... you know, that birdbrain who stumbles across this blog, entertains us with imbecilic comments over several days or weeks and then finds something new to drool over. I wouldn’t want to have to bin you with him. But ...

Here we have a scientific study that asserts - based on experimental data - that discrete genetic clusters exist at both the continental and subcontinental levels, and that individuals can be “binned” into their self-identified race with ~ 100% accuracy. Furthermore, admixture can be detected.

In response you, my liberal friend, promptly spew forth an opinion of how different groups’ looks blend into each other or some such nonsense.

Well, OK ... the western tradition of scientific empiricism smacks right up against the eastern traditions of mysticism (I noted well Larry’s religious bent in previous comments).

Race is real, race is proven, and anyone who doubts it can always be DNAPrint-tested and find out for themselves how
real the “illusion” is.

Posted by JW Holliday on October 03, 2005, 06:16 PM | #

Interesting. A few posts back, Larry was essentially telling us that we would burn in hell as racists. In the IQ post though he has been transformed into a “deist” who spouts warmed over Nietzschian philosophy (are you reading Zarathustra, Larry?), with a hyper-individualist Randian bent.

One wonders what the next mental spasm will produce?

What of course is not being produced in any of his comments is reasoned argument, backed up by facts. Relaying to us his preferences, his opinions, and what he “feels” is not of interest. Of course, for those of weak mind, the product of the self-centered materialism of the modern age, what they “feel” is equivalent to reality.

Maybe Larry is a believer in Solipsism. He certainly behaves that way.

Larry, Larry - I hate to tell you this, but your own mind is not the entire universe.

Posted by James Bowery on October 04, 2005, 12:03 AM | #

Ooops… liberallarry’s a liar.

According to Cavalli Sforza et al the Fst between European nations averages around 1%. The average Fst between European nations and Turkey is 8%. Even the Greeks who are at the low end of genetic distances from the Turks are at 7.94%.

Posted by James Bowery on October 04, 2005, 12:42 AM | #

We know DNAPrint is totaly out of whack simply by looking at the geographic distance vs genetic distance graphs for various continents in “On Genetic Interests” p 209. DNAPrint uses low-latitude Amerindian samples as representative of all Amerindians but of all the continental groups, Amerindians have the greatest Fst gradient by geographic distance.

Posted by Tom peters on October 04, 2005, 02:57 AM | #

“I would contend that race is an illusion.”

Race is an illusion to ‘liberals’ until it comes to affirmitive action. Race is an illusion to ‘liberals’ until it comes to them pointing out alleged historical wrongs and using guilt tactics and intimidation tactics to make gains for specific racial/ethnic groups. Race is an illusion to ‘liberals’ until they start demanding equal or better representation of racial groups in government/economics/power structures. Race is an illusion to ‘liberals’ until they use their demographic numbers to force their group agenda. Race is an illusion to ‘liberals’ until they start arguing/demanding why certain races don’t get enough TV time/spotlight/money/etc. Race is an illusion to ‘liberals’ until it comes to forming their own NCAAP, La Raza, ADL, etc. protection/group interest advancing group.

Shall I go on?

While it is nice to have scientific studies on this topic, it is also kind of sad that white nationalists cannot win the argument on common sense alone. Do we really need to have a study to ‘prove’ that whites and blacks are different? Do we really need to have studies to ‘prove’ that ethnic groups who claim to see no race in one instance but are ultra-sensitive to race issues in other instances are hypocritical?

Maybe I am just naive…

Maybe I wish whites were a little more observant when it came to these issues.

Having said all that:
I do see value in these studies - I just wish I saw more common sense and survival instinct in whites.

Posted by JW Holliday on October 04, 2005, 05:19 AM | #

As has been often stated - including by myself - DNAPrint has done a poor job with some of their parental populations. The Amerindian story is old news; obviously a group of Amerinds from southern Mexico does not cover the full spectrum of Amerind gene frequencies, which is why people with North Amerind heritage sometimes get some “East Asian” results with ABD testing. Given that DNAP is now wasting their time developing an Amerind-specific test, perhaps they’ll straighten that out.

But there is a deeper problem here. I’ve made an effort over the last few months to carefully dissect the strengths and weaknesses of the DNAPrint tests, and have voluminously posted and commented with respect to this. I’ve concluded that that the tests are, at best, mediocre as measurements of actual, direct, absolute ancestry (after all, if Pakistanis can test as 30% Amerind, one cannot depend on that for an actual measure of Amerind ancestry). However, as a comparative, relative measurement of individuals and groups vs. other individuals and groups in the proportions of the designated genetic components (which in some cases does give useful background on ancestry), the tests are excellent. That the tests work at ~100% accuracy in determining majority race is known by empirical blind study. That they work to discern relative minority affiliation is also determined by, eg, the correlations of genotype and phenotype among Mexicans and Filipinos, as well as the broad outlines of genetic gradients in the ethnic data,

But, this has already been discussed here. Thus, one wonders why facile blanket condemnations of the test are still made.

If there are data, apart from the odd anecdotal outlier, showing that the tests are wrong based upon the conservative intepretations I have outlined - in detail - on this blog, I’d like to see these data. If not, other questions need be asked.

Posted by James Bowery on October 04, 2005, 11:13 AM | #

If there are data, apart from the odd anecdotal outlier, showing that the tests are wrong based upon the conservative intepretations I have outlined - in detail - on this blog, I’d like to see these data. If not, other questions need be asked.

Perhaps I am too harsh—especially given DNAPrint’s environment—which include the likes of liberallarry making the noises he’s making. But I’ll put my reaction like this:

When DNAPrint first came out with their test and started explaining their methods, they made frequent reference to their “proprietary” techniques for clustering rather than offering a clear description of how they clustered their data. Then when I looked at the parent population sampling and the very first thing I noticed was the ridiculous use of low-latitude Amerindians as representative of the entire range. I saw them offer no explanations, no apologies and no estimate of the magnitude of resulting measurement error. This seemed inexcusable to me and I have since dismissed them as rather fast-and-loose with the data.

I’m very impatient with people who sit on top of vast amounts of data that they won’t publish, purport to estimate people’s EGI and then make errors so obvious that even I, a rank amateur, can casually pick them out.

PS: Another big problem here is that publishing your analyses in MR is not a good way to get them exposed. MR articles get shoved down to the bit bucket rapidly and there is too much stuff to sift through to find the meaty analyses such as you purport to have offered.

Posted by JW Holliday on October 04, 2005, 04:19 PM | #

James,

First, let me say that I share your frustration with the people at DNAPrint. They’ve made serious mistakes in the parental populations, they do indeed “sit” on data, they hide behind “proprietary” information, and often cop an attitude of “we’re the experts ...”

Thus, I will not defend them and how they’ve mismanaged the technology.

On the other hand, separating the technology from the people behind it, I think it works well given conservative interpretations.

For example, a quick search on MR using “DNAPrint” coughed up this post, just one of several posts on this subject I’ve made.

My hope is that DNAPrint will improve heir product and give more information. I’ve heard heresay evidence that another group may be trying to put together a microsatellite based race test. However, given the Yang article, I still think SNPs would be superior. Given that DNAP has, or is in the process of, patenting their markers and algorithms, I will await improvements.

They could always start by listening to so-called “amateurs” such as we on this blog who attempt constructive criticisms.

Posted by James Bowery on October 05, 2005, 01:17 PM | #

BTW: I’ve been running a series of blog entries at the collaborative site kuro5hin.org, based on your questions for anti-racists. That site is inundated by anti-racists so I figured it would be good to post the questions there since the GNXPers won’t respond. Here are the links:

Anti-Racists: Is the US Racist?

Anti-racists: Are Ethnotowns Permissible?

Anti-racists: Are white ethnic genetic interests legitimate?

Anti-racists: Are migration restrictions legitimate?

Anti-racists: If “diversity"is such a strength…

Anti-racists: Separatism vs Supremacy?

I’ve also started a series prefixed by “Anti-racist fallacies:”. The first is:

Anti-racist fallacies: Race is merely a social construct

Posted by Fred Scrooby on October 05, 2005, 09:39 PM | #

Look whom the police are officially classifying as white

nowadays.