ibd and historic mating patterns in europe

**update 08/03: post fixed to remove references to roh which i got wrong (roh≠blocks of ibd!) — see comments below (thanks, citrus!)**

princenuadha points me to this awesome pdf which i guess was a presentation given at a society for molecular biology and evolution (smbe) conference last weekend (thanks, prince!).

here is an interesting graphic from the presentation (pg. 21):

what this map shows are the means of runs of homozygosity (remember those?) blocks of identity by descent (ibd) that are greater than 1cM for each of these european populations. the longer the ibd blocks, the greater the identity by descent, and vice versa. small circles=fewer long blocks of ibd; large circles=more long blocks of ibd.

if a population has lots of short blocks of ibd, then its genetics are all mixed up, possibly due to outbreeding or because of a fairly recent mixing with another population. if a population has lots of long blocks of ibd, then its genetics are not so mixed up and the individuals within it share a lot of identity by descent. this can be an indicator of having been squeezed through a bottleneck or close inbreeding over time.

here are the mean numbers of long blocks of ibd for some of the countries on the map:

as you can see, my “core europeans” (english, french, germans, dutch, prolly some others) all have low means of blocks of ibd. the smallest circles are found right in the center of nw europe: england, france, belgium, germany. also italy (more about that below). in the immediate periphery around core europe, the circles are a bit larger, i.e. there are more long blocks of ibd: scotland, ireland, spain, portugal, switzerland, greece, scandinavians. eastern europeans have even larger circles/even more long blocks of ibd: poles, russians. and populations in the balkans, like the albanians, have enormous circles, i.e. LOTS of long blocks of ibd.

all of that fits the pattern i’ve been talking about here on the ol’ blog (see the mating patterns series below in the left-hand column): that the core europeans have been outbreeding the most and for the longest, with peripheral europeans lagging behind that trend, and eastern europeans really lagging behind the trend. i haven’t actually discussed the balkan populations (yet), but i do know that cousin/endogamous marriage rates are pretty high in the balkans.

i wonder if the numbers for italy may be unrepresentatively low, but it’s difficult to know. the data used are from popres and, like so much genetic data out there, have no provenance info attached to them. so, are the italian data from northern italy (which has a long history of outbreeding) or southern italy (which has a lot of inbreeding) or a combination of both? dunno.

this is a very cool study! i like it a lot. (^_^)

polish gen also has an interesting post about the presentation, btw.

(note: comments do not require an email. ruh roh!)

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28 Comments

  1. Excellent find! You and those who discuss your work, like myself, have been talking about the inbreeding/outbreeding thing for awhile. Now we have it roughly quantified! And it fits the pattern you’ve described very well (the Balkans are like “holy homozygosity, Batman!”). There are some interesting oddballs. Italy is obviously one; I’d bet that that datum is either averaged over the whole country (where the lower population of the south would drown out) or from northern Italy alone. Also, Sweden is more inbred than Portugal or Ireland? And what is going on in Greece and Turkey? I wish they did more regional comparisons in Iberia and Italy.

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  2. Africans are the most heterozygous population.

    With greater panmixia the world is being gradually Africanized. This results in a tendency toward greater polygyny, greater disparity of wealth and other disparities, such as disparities of IQ, resulting from greater general heterogenity leading to heterozygosity of the population. This raises the stakes for being an alpha male tremendously. The game females must play here is similar to the game African females must play: Self-sufficiency and selection of the most dominant (genetically and socially) alpha male for his genes, with an occasional tryst with a beta male to keep them from killing the kids.

    There’s a transition — over the course of a single generation — from a predominantly monogamous, lifetime companionate family structure, to “serial monogamy” which really is serial polygyny, given the progressive centralization of male fertility resulting from it. Islam offers a relative compromise, supporting open polygyny with hard limits (4 life-time wives maximum). This may be why it is such a threat to the West — which has a rather unstable mix of global panmixia and serial polygyny with bountiful opportunities for free-riders.

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  3. @luke – “What would it look like for the U.S.? Dots?”

    yeah, lots o’ dots.

    except maybe some parts of the country like the eastern u.s. where there’s been longer settlement and esp. in areas settled by families (new england, appalachia). maybe amongst the mormons, too? (maybe not.) also, areas where there are a lot of mexicans ought to show up as larger dots/circles since they are a population characterized by having long roh in general.

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  4. @g.w. – “Very neat fit – mostly.”

    @jayman – “And what is going on in Greece and Turkey?”

    yeah, it’s not a perfect fit because other processes aside from inbreeding/outbreeding can affect the “variety” of genes in a population, like in-migration. so i think that the low numbers of long roh in greece & turkey reflect the fact that they are right there at the crossroads between europe and asia minor where populations have been traipsing back and forth since before the agricultural revolution.

    it is a very neat fit, though. (^_^)

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  5. @jayman – “the Balkans are like ‘holy homozygosity, Batman!'”

    ha! (^_^)

    yeah, those populations really put the “balkan” in “balkanization”!

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  6. @jayman – “There are some interesting oddballs. Italy is obviously one; I’d bet that that datum is either averaged over the whole country (where the lower population of the south would drown out) or from northern Italy alone.”

    it’s almost impossible to know which part or parts of italy are represented here.

    the data are from popres which you can read all about here.

    i guess that the samples for italians come from either the london life sciences population study (LOLIPOP) and/or the duke university healthy volunteers study. if some/all of the italian samples are from the duke study, then those genomes might not, strictly speaking, be representative of how things are on the ground in italy since the italian-americans in the study might be products of inter-breeding by northern and southern italians in the u.s. *facepalm*

    otoh, maybe italians really don’t have many long roh. if so, that’s interesting and needs explaining.

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  7. @jayman – “Also, Sweden is more inbred than Portugal or Ireland?”

    could have to do with less genetic diversity in the past in sweden than in ireland (don’t know about portugal). the population for the whole of scandinavia in the 1300s — and that’s at its height for the medieval period — is reckoned to have been just 2 million, whereas i’ve read somewhere (can’t recall the reference) that the early medieval population in ireland was as high as 8 million people.

    more people, more chances of diversity in the population’s genomes. that could be reflected in today’s populations.

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  8. @g.w. & jayman & everybody – i forgot to say, make sure to have a look at the original presentation ’cause the author/s argue that the patterns in the data reflect migrations in europe like the germanic ones and the huns as well. pgs. 43-46 especially. i think they’re prolly right, too.

    neat stuff! (^_^)

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  9. “could have to do with less genetic diversity in the past in sweden than in ireland (don’t know about portugal).”

    Yeah, that does kinda get in the way of what is almost a cousin marriage map : )

    Though it is cool to compare countries of more similar heritage.

    England to Ireland and Scotland. Germany to Poland. Spain to Portugal. Etc…

    “And it fits the pattern you’ve described very well (the Balkans are like “holy homozygosity, Batman!”).”

    Haha, totally. That’s something that really jumped out at me.

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  10. @princenuadha – “How do I ‘log in’ and avoid this moderation stuff? Just use an email?”

    sorry. i’ve got partial moderation on at the moment — it’s just a precautionary/temporary thing. i’ll prolly take it off in a couple of days.

    if you leave a comment from the same ip address each time, i should only have to approve the first one, and then all the rest should be auto-approved. if you’re using a proxy or go to another computer … sorry!

    edit: maybe you have to have cookies enabled? not sure how it works, to tell you the truth.

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  11. Jake wrote: “Africans are the most heterozygous population.”

    I’ve heard that Ashkenazim are also more heterozygous than Europeans. And that Ashkenazim are genetically around 4th or 5th cousins among each other. How does that work? When 2 random Ashkenazim get married, isn’t that kind of like cousin-marriage (though obviously not as close as 1st cousin-marriage, but still a kind of cousin marriage)?

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  12. @bysshe – “When 2 random Ashkenazim get married, isn’t that kind of like cousin-marriage (though obviously not as close as 1st cousin-marriage, but still a kind of cousin marriage)?”

    absolutely!

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  13. @szopeno – oh, it’s all very recent/modern — not older than, you know, teh scientists have been sequencing genomes. the data come from different sources — you can read all about them here.

    it’s not fully clear to me where the polish data come from. must be either the london (LOLIPOP) and/or duke university studies. -?-

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  14. “i haven’t actually discussed the balkan populations (yet), but i do know that cousin/endogamous marriage rates are pretty high in the balkans”

    No not really. The Balkans had the 7th cousin law, that forbid them to marry anyone closer than the 7th cousin.

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  15. @nick – “The Balkans had the 7th cousin law, that forbid them to marry anyone closer than the 7th cousin.”

    unlikely. but if you’ve got a reference, i’d love to see it!

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  16. @citrus – “IBD has nothing to do with runs of homozygosity (roh), please read the paper….”

    i did read the paper, but perhaps i misunderstood.

    this is how the authors described their “ibd blocks”:

    “We define an ‘IBD block’ to be a contiguous segment of genome inherited (on at least one chromosome) from a shared common ancestor without intervening recombination…. Suffciently long segments of IBD can be identified as long, contiguous regions over which the two individuals are identical (or nearly identical) at a set of Single Nucleotide Polymorphisms (SNPs) which segregate in the population.”

    how are those not roh? are roh by definition precisely identical and ibd blocks not really? or is/are there some other difference/s?

    if i’m wrong, i’ll certainly correct my post! thanks!

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  17. Perhaps it would be best to ask the authors themselves, but basically roh means that individual A has continuous regions of DNA where BOTH DNA strands – paternal and maternal – are identical to each other. IBD block means that individual A and individual B match each other on only ONE of the DNA strands. It does not mean that both their strands are identical, which would be roh.

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  18. @citrus – “It does not mean that both their strands are identical, which would be roh.”

    ah ha! gotcha! thank you very much! (^_^) i’m gonna take your word for it and just fix the post accordingly.

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  19. I’m wondering if this data has been compared to rates of diseases? I’ve often pondered if there are any correlations…

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  20. @rachel – “I’m wondering if this data has been compared to rates of diseases? I’ve often pondered if there are any correlations…”

    dunno! what sorts of diseases/correlations were you thinking of?

    Reply

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