The genetic map of Europe we already knew….
From Henry Harpending:
This is from a 1984 paper, citation below the figure. The genetic data were 6 red cell antigens, 9 electrophoretic systems, and HLA and HLB. The context was the authors’ effort to set up a big population genetic and demographic database of Mormons, which was criticized because the Mormons were thought to be derived from a small isolated inbred group. They wrote this paper to show that Mormon allele frequencies were generic northern European. Another paper the followed this showed that Amish and Mennonites were indeed off in another dimension, but not Mormons.This isn’t up to current standards but it does show that 25 years ago the correspondence between genetic and geographic distances in Europe was clear.
McLellan T, Jorde LB, Skolnick MH. 1984. Genetic distances between the Utah Mormons and related populations. Am J Hum Genet 36:836-857.
I made a minor modification to the figure, which is courtesy of Lynn Jorde.
Labels: Genetics
As a Pole, I feel lonely, too.
Not surprisingly, the average American’s DNA seems to be a cross between British Isles and Germanic. The Mormon DNA is different; maybe more English.
But where are the pretty colors and shapes?
Is anyone else having a problem with the text of this post flowing properly in their browser?
The right pane is covering the text in all the posts in my browser currently. But in previous posts i can click on the post link and bring them up properly. No so this one. I think the graph dropped in keeps the text pushed right and underneath the right pane … it’s a pain.
If someone has had this problem and dealth with it someone, please give me a holler.
I’m afraid that the webpage looks a terrible mess on my laptop (using IE6).
It looks fine in Firefox, but all messed up in IE6.
Pub Med has a PDF of the full article if anyone is interested.
I think IE6 is all messed up as a browser. Try IE7.
I noticed that the chart of various nations roughly corresponds to their geographical locations. Any reason for that?
http://www.23andme.com has its own version of the genetic map. You can see it by going to “Global Similarity” and clicking on “advanced view”. The map has several different views. As I understand it, if you switch to the “European” view, it doesn’t just zoom in on the world plot, it recomputes the coordinates using only European reference populations. The reference populations they’ve used look as through they might be the ones from HGDP.
Their example individual, known by the pseudonym “Greg Mendel” is placed close to the English, French and German clusters by this algorithm (they’re not well-separated on the 23andme map). He’s reasonably clear of the Irish, Orcadian and Austrian clusters.
I’m half expecting someone to make a joke about me being a Neanderthal. These maps suggest that new alleles diffuse across Europe rather slowly. If any of homo sapiens have a few surviving Neanderthal genes, it’s most plausible in someone from the western edge of Europe like me.
link
link
I’ve been looking somemore at the SNP’s listed in table 2 of
paper by Heath et al.
I took the SNP’s that didn’t show statistically significant geographical
variation in Hapmap phase II (CEU, CHB,JPT, YRI), and looked to
see if there was significant variation between the Hapmap phase III
populations. Phase III looks at more populations, so has a better chance
of detecting variation that is more geographically localized, or that
requires a bigger sample to detect.
As I’m looking at several datasets until I find one that gives statistically
significant results, you need to take account of this multiple testing when
interpreting p values.
rs1473602. Gene IRF4. chi2=29.55
G is more common in CEU than other populations.
Nearby SNP’s that have been the subject of association studies include
rs12203592 (black vs blond hair), rs12203592 (black vs red hair),
rs872071 (leukemia), rs150771 (freckles).
rs7047524. Gene DMRT1. chi2=14.7.
Retain the null hypothesis that there is no geographical variation
in allele frequency.
rs4803866. chi2=40.05
Frequency of C lower in GIH and MEX. Hapmap phase II doesn’t contain
any samples from India or of Native Americans, so that may explain why
it didn’t detection this local variation.
Conclusions
a) Apart from rs7047524, these SNPs all showed geographic variation
on a global scale. It might be worth checking rs7047524 against other
datasets to see if the within-Europe and within-UK variation reported
by Heath et al is real or a chance fluctuation in their data.
b) Hapmap phase III is giving us added value here. There seems to be geographic
variation specific to Indian or Native American samples that the 4 original
Hapmap samples miss. (MEX is “Mexican Ancestry in Los Angeles”, which presumably
includes some Native American ancestry).
susan, can you email me at razib – at- gnxp – dot – com ?