Saturday, May 14, 2011

Height, breeding values and selection

I can't wait to read this paper. The results were reported on the blog Genetic Inference, based on a talk at Biology of Genomes 2011.

A few comments:

1. Although known alleles for height only account for 5-10% of variance (out of the expected 80-90%), it is very plausible that loci of smaller effect or MAF (minor allele frequency) account for the "missing heritability". We still lack sufficient statistics to detect most of the individual loci of this type, but it's a matter of time. See beautiful paper from Visscher's group. The results described below suggest that loci just below the (arbitrary) significance threshold currently in use might also be height associated. There is a whole distribution of loci with smaller effect sizes and MAF that are just waiting to be discovered -- we have only found the tip of the iceberg.

2. Even with only a fraction of total additive variance identified, one can still make estimates of breeding value for groups by simply computing the prevalence of known associated loci in each group. How indicative these (large effect/MAF) loci are of the actual breeding values can't be answered a priori, but I would bet they are a good indicator, and this seems to be the case for height.

3. If the results on selection hold up this will be clear evidence for differential selection between groups of a quantitative trait (as opposed to lactose or altitude tolerance, which are controlled by small sets of loci). We may soon be able to conclude that there has been enough evolutionary time for selection to work within European populations on a trait that is controlled by hundreds (probably thousands) of loci.

4. With luck we might get to this level of analysis for g in the next 5-10 years. (I originally wrote 3-5 years but one of my more sober collaborators convinced me that would be quite unlikely!)

5. Understanding the evolution and distribution of quantitative traits like height and g at this level is an important milestone in scientific history.

It's amazing to see scientific and technological progress verify models that you've had in your head since age 12 :-)

Genetic Inference: ... Europeans differ systematically in their height, and these differences correlate with latitude. The average Italian is 171cm, whereas the average Swede is a full 4cm taller. Are these differences genetic? Have they been under evolutionary selection in recent human history?

Michael Turchin gave some pretty convincing answers to these questions, using genetic data from the 129 thousand individuals in the GIANT consortium. He compared the frequencies of alleles that are known to increase height, and found that they are more common in Northern Europe. Interestingly, he found the same relationship for alleles that have weaker evidence for height association, showing that there are still a large number of common height variants hiding in the genome, which are also more frequent in Northern Europe.

Height differences are thus heritable, but have they been under evolutionary selection? Or are these differences merely down to genetic drift? This can also be tested using the GIANT data, which shows significant statistical evidence of selection on height variants in recent history. On top of that, the magnitude of the selection is correlated with the effect size of the height variant, providing strong evidence that these variants are being selected specifically for their impact on height.

This is a textbook example of how an evolutionary study should be done; you show a phenotypic difference exists, that it is heritable, and that it is under selection. This opens the question as to why height has been selected in Northern Europe (or shortness in Southern Europe). Could the same data be used to test specific hypotheses there?

14 comments:

MtMoru said...

"He compared the frequencies of alleles that are known to increase height, and found that they are more common in Northern Europe."
 
That are known to increase height in what popualtion under what circumstances?
 
"With a little luck we can probably get to this level of analysis for g in the next 3-5 years."
 
There's a big problem here. g is not first a characteristic of individuals as height is. It is the projection of an individual's scores on a batttery onto the pricipal component of the population the individual is a member of. Needless to say this obvious observation has eluded "pyschometricians". Furthermore for a large enough battery the pricipal component is inadequate, see Peter Schönemann.

The analogy of height and IQ or any other psychological trait is tiresome.

steve hsu said...

Hello anon. You can stay if you can behave.

The dominant pca vector that is g does not vary significantly between populations, at least according to the limited data available (pretty significant for western countries and Japan). Once we fix this vector then g is a property of the individual.

You can read the GIANT papers if you want to know more about the population under study, but basically we're talking about affluent europeans.

MtMoru said...

Oh no you misunderstood me. I'm sure the PC is nearly the same for all populations.

The problem with g is that it is a statistic, a characteristic of a population or the whole population of the planet if you prefer. It is not first a characteristic of indivuduals like height.

I guess it really is a subtle point.

I made a comment here a few months ago and you referred to me as "anon". What does that mean? 

MtMoru said...

The N/S thing is misleading. Europe's tallest people live in the Dinaric Alps. Many of them are Muslims! 

ben_g said...

g might be hard to compare between populations, to the extent that different genes are better for intellectual development in different environments (by the way, how do we know it's not like that with north vs south italians here?).  i guess you could rule that out by replicating a GWAS in multiple populations.

Keith Power said...

"This opens the question as to why height has been selected in Northern Europe (or shortness in Southern Europe)."

Easy - tall Swedes are better looking than short ones, short Italians are better looking than tall ones ;-)

Henry Harpending said...

MtMoru 

The correspondence between height and IQ is not so different: height is a linear combination of 1*(heel +tibia+femur+pelvis+trunk+neck+head), or something like that, which is arbitrary in its own way.  We can parallel much public criticism of IQ with the same criticism of height.  For example height is not a single thing, it is a combination of many things that can vary independently.  Some people have long legs, some have high heads, ergo we cannot speak of "height."   And sure enough there may be a better linear combination of those variables, better for some purposes.  Any quantitative trait is subject to the same sort of chatter.

It is true enough that apparent selection for height may in fact be selection for something else genetically correlated with height.  Selection on a quantiative trait is selection in some direction in a high dimensional space and there is no (apparent, to me) easy way to find just what that direction is.  Same for IQ.

steve hsu said...

Sorry if I mistook you for someone else. There is a commenter here who often changes his pseudonym. He went by anon for a long time.

Edwin said...

Hi steve,am a lowly undergraduate with very limited mathematical tools,so be patient with me.For over 5 yrs i have been wrestling with these  excerpt from Plato's the Republic(Book VIII),"Now that which is of divine birth has a period which is contained in a perfect number, but the period of human birth is comprehended in a number in which first increments by involution and evolution (or squared and cubed) obtaining three intervals and four terms of like and unlike, waxing and waning numbers, make all the terms commensurable and agreeable to one another. The base of these (3) with a third added (4) when combined with five (20) and raised to the third power furnishes two harmonies; the first a square which is a hundred times as great (400 = 4 X 100), and the other a figure having one side equal to the former, but oblong, consisting of a hundred numbers squared upon rational diameters of a square (i. e. omitting fractions), the side of which is five (7 X 7 = 49 X 100 = 4900), each of them being less by one (than the perfect square which includes the fractions, sc. 50) or less by two perfect squares of irrational diameters (of a square the side of which is five = 50 + 50 = 100); and a hundred cubes of three(27 X 100 = 2700 + 4900 + 400 = 8000). Now this number represents a geometricalfigure which has control over the good and evil of births."Does this make sense to you?figure which has control over the good and evil of births."Does this make sense to you?

MtMoru said...

HH:

Height is not arbitrary. It is observed quite easily. It is not calculated as a linear combination of heel, tibia, femur, etc. Height is not misleading, because it is something in its own right. There is no need to measure heel, tibia, femur, etc. in order to determine height.

Why bother with the arbitrary, population determined, mapping from the individual trait (the subtest scores) to a single parameter? Why not just regress on the space of subtests?

g is very basically an attempt at sounding much more "scientific" than intelligence research really is.

Really just jesuitry.

By the way Henry have you ever read tractate Abot?

MtMoru said...

If you're really interested in psychometrics you should read this:

http://www.schonemann.de/pdf/89.pdf.

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