hgdp samples and relatedness

**update 03/22: see follow up post — more on the hgdp samples — and just ignore what i said about the french samples below.**

**update 08/28: ignore what i said about ignoring what i said about the french samples. see here.**

i had a post up back in january about some cool research that looked at what runs of homozygosity (roh) in samples from the human genome diversity project (hgdp) can tell us about the inbreeding or outbreeding of different human populations.

but i’ve been bothered by the thought of how the hgdp samples were gathered. as professor harpending said:

“No one knows, by the way, how sampling was carried out for this nor for any of the HGDP populations.”

ugh. the hgdp is really, really cool — but not having info on where the samples came from — like genealogical info — poses a problem if you want to use this data to look at recent inbreeding/outbreeding or, i think, even the sort of thought experiment that prof. harpening conducted a couple of weeks ago, however cool that was, too.

here’s an example of what i mean.

prof. harpending compared the relatedness or kinship of the individuals in a couple of sets of samples from the hgdp: the french, the japanese, and the druze. he found that the kinship of indviduals in both the french and japanese populations to their nearest “relatives” (i presume two individuals who had the most similar genomes?) is very similar. as he said: “from the viewpoint of kinship, one person is not very different from another person.” the druze, otoh, are very dissimilar and the good professor thinks that this is a population in which “opportunities for discord and clannishness are high as individuals able to discriminate kin would ally against the ‘others.'”

i’m not going to argue with that! the druze, like the arabs, regularly practice father’s brother’s daughter (fbd) marriage, the most incestuous form of cousin marriage around, so i’m not surprised that their genomes reflect this fact. (fbd marriage probably originated in the levant, so it could be that the people who are today known as the druze are the product of one of the longest running close-inbreeding projects in humans around.) amongst the druze, each extended-family or clan must’ve become, over time, it’s own little semi-isolated sub-group. like the arabs, i’d expect a lot of clannishness and infighting.

however, wrt to the french and japanese samples: the ceph folks do have some information on the hgdp samples, and one point of difference between the french and japanese samples is that the french samples are described as having been drawn from relatives whereas the japanese samples were not.

there are 29 french samples described as: French (various regions) relatives, and there are 31 japanese samples described as just Japanese, so i assume that means the japanese samples do not include relatives.

so what does French (various regions) relatives mean? i guess that the samples were drawn from different regions of france, but we don’t know which regions or how many. (which is too bad because different regions of france have, historically, had different inbreeding rates.) and how many relatives? who knows? i’m going to presume all 29 are not relatives from one family living scattered across the country, although i suppose that could’ve been the case. what seems more likely to me is that we’re looking at groups of samples from a number of different families, but how many? two, three, four … ten? again, who knows?

what difference would this make? well if the kinship in the french set of samples and the japanese set of samples look to be around the same, i.e. “one person is not very different from another,” BUT the french samples are from relatives and the japanese samples are not, then that would mean that the individuals in the broader french population must be even more like one another than the individuals in the broader japanese population since french family members have the same kinship to one another as japanese strangers do.

to put it more simply, comparing the french and japanese samples is like comparing apples and oranges because, if the ceph information is correct, the french samples include family members whereas the japanese ones do not.

the druze samples, too, are described as coming from relatives — again no info as to how many families/relatives — so the broader druze population should prove to be even more dissimilar to one another than these family members are.

i would love to see lots more studies done on inbreeding/outbreeding (and possible inclusive fitness-related behaviors) in human populations from a genetics p.o.v. — like what prof. harpending did in his recent post. but afaics, using the hgdp data is problematic. i look forward to when there are more whole genome sequences available out there WITH accompanying genealogical/pedigree information.

previously: runs of homozygosity and inbreeding (and outbreeding)

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  1. The North American whites in the HGDP sample are from Utah, right? Lots of Mormons, presumably. So, they are probably a selection of Northwest Europeans who got mixed up considerably in the 17th to 19th Century in relocating to the U.S.


  2. @steve – “The North American whites in the HGDP sample are from Utah, right?”

    they’re actually part of hapmap not the hgdp, but yeah — a good number of them seem to be mormons. i’ve been meaning to go through the list of all of them to see how many are mormons — just out of curiosity — but haven’t gotten around to it yet. it’s on the “to do” list on the fridge, tho. (~_^)

    like you say, probably a mixed up selection of nw europeans — certainly not representive of europeans — which then must’ve gotten narrowed down again a bit genetically speaking ’cause of the polygamy, but i have no idea how much polygamy actually happened in the mormon population.


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