March 29, 2009
Genetic Copy Number Variations Compared Between Races

A recent research report entitled "Copy number variation in African Americans" looks at racial differences in DNA sequence differences for what are called copy number variations (CNVs). A CNV is where a big stretch of DNA gets duplicated 1 or more times in some but not all people. CNVs can amplify the expression of a gene by making more copies available for translation into peptides and into regulatory sequences. CNVs are a big deal.

Joseph P McElroy and colleagues from the Department of Neurology, University of California at San Francisco, recruited African Americans from 28 States and used their genomes to draw CNV comparisons with the White dataset. "To the best of our knowledge, this is the first detailed map of copy number variations in African Americans. Understanding the distributions of CNVs in a population is a first step to addressing their role in disease".

The authors employed an array of over 500,000 sequences whose position in the human genome is already known due to single nucleotide polymorphisms. They first analysed the interaction of 50 blood samples of healthy African American females with this gene chip platform, and then used the results as a reference to assess copy number variation in samples from a further 385 African Americans, and an additional set of samples from 435 White individuals. In total, 1362 CNVs were detected in African Americans and 1972 in the White cohort. Across most of the genome, the frequency of CNVs did not differ greatly between the two populations. However, there were two duplications, one on chromosome 15, and one on chromosome 17, whose frequency varied markedly between the two groups.

The research team discovered that the duplication in chromosome 17 (region 17q21) is present in 45% of White but only in 8% of African American individuals. Another independent study has implicated the same region in mental retardation caused by a deletion due to duplication. Among the deleted genes, two of them, CRHR1 (corticitropin releasing hormone receptor 1) and MAPT (microtubule-associated protein tau), were previously associated with some neurological disorders. These two genes are not contained within the 17q21 region of CNV duplication, but map very close to it.

Geneticists are way ahead in identifying genetic differences in contrast to their understanding of what the differences mean. Also, geneticists know more about single letter genetic differences (single nucleotide polymorphisms or SNPs) than they do about these copy number variations (CNVs). The technology for detecting SNPs advanced sooner than the technology for detecting CNVs. But now we are at a point where the costs of detecting SNPs and CNVs are plummeting and we can expect a huge flood of data on genetic differences in the next several years. We can also expect a big flood of discoveries for what it all means. Prepare yourself for a big change in our understanding of human nature and human evolution.

Here is the open access paper in BMC Genetics.

An excellent recent book, The 10,000 Year Explosion: How Civilization Accelerated Human Evolution, argues that human evolution accelerated by a factor of 100 over the last 10,000 years and that humans have undergone substantial amounts of natural selection to adjust for local conditions. So some of the large copy variations discovered above which are specific to one race or the other probably adapted our ancestors to local conditions in a variety of fashions including toxin processing, immune response to local diseases, digestive adjustments to locally available foods, adjustments to climates, and assorted other adaptations.

Share |      Randall Parker, 2009 March 29 09:56 AM  Trends, Human Evolution

James Bowery said at March 29, 2009 2:13 PM:

Whatever happened to Lewontin? I don't mean as in Lewontin's Fallacy -- for it seems what is being claimed here, and what is being claimed by H&C, put secondary Edwards' critique of Lewontin's infamous "more variation within than between groups" critique of race classifications.

Also, I would have liked to have seen H&C talk a _little_ about measuring genetic correlation structures that might have arisen during the 40,000 year period prior to the 10,000 year explosion, rather than merely grouping them with more obviously "complex adaptations" the way Tooby and Cosmides do. I mean we are on a continuum here after all.

James Bowery said at March 30, 2009 7:13 AM:

Actually my comment should be modified, as should Edward's critique of Lewontin, to have a place for the phrase "phenotypic correlation structures", because some of the times people use "genetic correlation structure" they are really talking about phenotypic correlation structure. This is important because H&C _do_ talk about genetic correlation structure in relation to race and recent adaptation, but the example they give is in terms of a single phenotype: the size of Great Danes vs Chihuahuas. "Complex adaptations" of the type I am interested in are synergistic genetic correlation structures -- made synergistic by virtue of the fact that the there are multiple phenotypes involved in realizing the adaptation.

I really think that when most people talk about Lewontin's Fallacy, they are intending to talk about "complex adaptations" aka "phenotypic correlation structures" because race is so obvious when we observe people's phenotypes. To quote Edwards from the key passage in Lewontin's Fallacy:

Cavalli-Sforza and Piazza(6) coined the word ‘treeness’ to
describe the extent to which a tree-like structure was hidden
amongst the correlations in gene-frequency data. Lewontin’s
superficial analysis ignores this aspect of the structure of the
data and leads inevitably to the conclusion that the data do not
possess such structure...
The statistical problem has been understood at least since
the discussions surrounding Pearson’s ‘coefficient of racial
likeness’(8) in the 1920s. It is mentioned in all editions of
Fisher’s Statistical Methods for Research Workers(1) from
1925 (quoted above). A useful review is that by Gower(9) in a
1972 conference volume The Assessment of Population
Affinities in Man. As he pointed out, ‘‘. . . the human mind
distinguishes between different groups because there are
correlated characters within the postulated groups.’’
The original discussions involved anthropometric data, but
the fallacy may equally be exposed using modern genetic

In my terminology a phenotypic correlation structure would have "treeness" at the genetic level due to the phylogeny of adaptations at the phenotypic (anthropometric) level. It is such phylogeny of tree-like adaptations that are of the greatest racial interest as "complex adaptations" during the 40,000 years preceding the 10,000 year explosion.

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