runs of homozygosity again

**update below**

here’s an exciting new paper!: Genomic Patterns of Homozygosity in Worldwide Human Populations. i don’t have access to the paper itself, but there are lots o’ neat figures and tables in the supplemental data [opens pdf] that relate to runs of homozygosity (roh). roh are identical stretches of dna within an individual’s genome (i.e. identical on each of the dna strands, paternally and maternally inherited). (roh shouldn’t be confused with blocks of identity by descent [ibd], which i did once! ibd blocks are identical stretches of dna as compared between different individuals, iiuc.)

recall that possessing lots of long roh indicates that one’s parents are/were quite similiar genetically speaking. that can be as a result of a couple of different genetic scenarios like (as greying wanderer has brought up a lot recently) simply being from a small sized population (i.e. having a small effective population size) and/or from regular inbreeding (consanguineous/endogamous mating). so, a population having a lot of long roh is either small and/or inbreeds a lot. populations having LOTS of short roh have probably been through some sort of bottleneck (see previous post).

in the paper i looked at in that previous post, the researchers had looked at the different roh lengths for large, regional populations like “europeans” or “east asians.” amongst other things, they had found that some of my regular inbreeders — the fbd marriage folks — had some of the highest numbers of medium and long roh, a state of genetic affairs which likely reflects their long-term close mating patterns. interestingly, the researchers had found that east asians had roh lengths similar to those of europeans across the board, something which surprised me since, at least according to what i’ve been reading, east asians (i.e. the chinese) have been inbreeding for a much longer time than europeans. one drawback of that previous study, though, was that, apart from the french, most of the european populations they looked at were peripheral groups who have had a tendency to inbreed more than my “core” europeans (see mating patterns in europe series below ↓ in left-hand column).

the new paper suffers from some of the same problems since the data come from the same sources (hgdp-ceph and hapmap phase 3 populations), so northern europeans — apart from the french — aren’t included in this paper either. (what can you do? it’s early days yet. i look forward to when there’s lots more genetic data available out there for teh scientists to work with! (^_^) )

what the researchers in this paper have done, though, is to look at both the different mean lengths of roh in each of the different populations sampled AND they looked at total numbers of roh within individuals for each population. this has, i think, drawn out some interesting differences between the populations.

first, here are two graphics from the supplmental data (linked to above). click on each for LARGER views (they should open in new tabs/windows — you might have to click on them again there to super-size them).

i’ve highlighted a handful of populations i want to focus on ’cause i know a little something about their historic mating patterns: the bedouin (as a proxy for the arabs — note that the bedouin have probably inbred more than more settled arabs); italians (not sure if they’re northern or southern italians or a mix of both — however, there are tuscans in the samples with which these “italians” can be compared); pathan or pastuns (more fbd marriage folks, like the bedouins/arabs); and han chinese (there are some northern han chinese with whom this groups can be compared). ok. here are the charts:

as you can see, the researchers have split up the roh into three classes (note that the short and medium classes here are a lot shorter than those in the paper looked at previously):

– A: 0.25-0.40 Mb (short)
– B: 0.6-1.2 Mb (medium)
– C: 0-35 Mb (long)

the interesting thing in the first chart above (Fig. S3 – Mean ROH Length for Each of the Three Size Classes in Each Population), is that the han chinese have lower means of roh length in all of the size classes compared to the other populations i’ve highlighted. in the previous study, the researchers found that east asians had similar means to europeans for all roh lengths. i found this surprising since, from what i’ve read, the han chinese have been inbreeding for a longer period of time than europeans. what might be confounding the results though, once again, is the fact that nw europeans (the outbreeders extraordinaire) are not really included in either of these studies apart from a handful of french samples.

in this latest study, both the bedouin and the pashtun, for instance, have higher means — and wider spreads — of long (class C) roh than the italians, which is what i would’ve expected since those two groups (the bedouins and the pashtuns) are, being fbd marriage folks, serious inbreeders. perhaps the reason the han chinese long roh mean is comparatively low is partly due to the fact that they historically practiced mother’s brother’s daughter (mbd) marriage which doesn’t push towards such close inbreeding as fbd marriage. still, i would’ve expected to see greater means of roh for the chinese than the italians — or, at least, around the same. not so much lower. (unless the italians practiced fbd marriage, too — or fzd marriage — but i don’t think so.)

if you look at the second chart (Fig. S4 – Total Number of ROH in Individual Genomes), however, you’ll see that, overall, the han chinese have more short, medium and long roh totally in individual genomes than any of the other three populations i’ve highlighted. both the bedouins and the pashtuns have greater numbers/wider total spread of long roh than the italians, but the han chinese have a much greater total number of long roh than any of the other three groups — three or four times as many.

but they’re, on average, shorter long roh don’t forget. (confusing, eh?!)

perhaps this is what you get when you have — as the chinese have had — a pretty good-sized effective population size for such a long time. there have been a LOT of han chinese for — wow — millennia.

so, it looks like this (in this order of inbrededness — i think):

– bedouins: highest mean, and very wide spread, of long roh; high total numbers, and widest spread, of long roh.
– pashtun: low mean, but widest spread, of long roh; low total number, but very wide spread, of long roh.
– han chinese: very low mean, and very narrow spread, of long roh; highest total numbers, and wide spread, of long roh.
– italians: low mean, and rather wide spread, of long roh; very low total number, and very small spread, of long roh.

other interesting points are that:

– the tuscans/tsi (toscani) appear to have lower short, medium and long mean roh than the generic “italian” category. however, the tuscans have lower total numbers of long roh than the “italians” while the toscani (tsi), on the other hand, appear to have a greater total number of long roh than the “italians.” while the tuscan samples and the toscani/tsi samples are from different studies (hgdp vs. hapmap), they are all supposed to be from tuscany, so it’s surprising that they’re so different. perhaps the individuals in the toscani/tsi sample were more closely related somehow?

– the northern han samples have lower short, medium and long mean roh than the generic “han” category. this would fit my general impression that historically inbreeding has been greater in southern china than in the north. however, the total number of long roh are greater in the northern han sample than in the “han” sample. not sure what that means.

don’t forget that there can be all sorts of reasons for differences in roh: inbreeding vs. outbreeding, yes, but also effective population size, population movement (migration in or out), bottlenecks, etc. i just happen to be interested in trying to pick out the effects of inbreeding/outbreeding — if possible.

**update – here are a couple of excerpts from the article (thnx, b.b.!) [pgs. 277, 279-281]:

“Size Classification of ROH

“Separately in each population, we modeled the distribution of ROH lengths as a mixture of three Gaussian distributions that we interpreted as representing three ROH classes: (A) short ROH measuring tens of kb that probably reflect homozygosity for ancient haplotypes that contribute to local LD [linkage disequilibrium] patterns, (B) intermediate ROH measuring hundreds of kb to several Mb that probably result from background relatedness owing to limited population size, and (c) long ROH measuring multiple Mb that probably result from recent parental relatedness….

“In each population, the size distribution of ROH appears to contain multiple components (Figure 2A). Using a three-component Gaussian mixture model, we classified ROH in each population into three size classes (Figure 2B): short (class A), intermediate (class B), and long (class C). Size boundaries between different classes vary across populations (Table S1); however, considering all populations, all A-B boundaries are strictly smaller than all B-C boundaries (Figure 2C). The mean sizes of class A and B ROH are similar among populations from the same geographic region (Figure S3), with the exception that Africa and East Asia have greater variability. The class C mean is generally largest in the Middle East, Central/South Asia, and the Americas and smallest in East Asia (Figure S3), with the exception that the Tujia population has the largest values. In the admixed Mexican population (MXL), mean ROH sizes are similar to those in European populations. In the admixted African American population (ASW), however, mean ROH sizes are among the smallest in our data set, notably smaller than in most Africans and Europeans.

“Geographic Pattern of ROH

Several patterns emerge from a comparison of the per-individual total lengths of ROH across populations (Figure 3). First, the total lengths of class A (Figure 3A) and class B (Figure 3B) ROH generally increase with distance from Africa, rising in a stepwise fashion in successive continental groups. This trend is similar to the observed reduction in haplotype diversity with increasing distance from Africa. Second, total lengths of class C ROH (Figure 3C) do not show the stepwise increase. Instead, they are higher and more variable in most populations from the Middle East, Central/South Asia, Oceania, and the Americas than in most populations from Africa, Europe, and East Asia. This pattern suggests that a larger fraction of individuals from the Middle East, Central/South Asia, Oceanis, and the Americas tend to have higher levels of parental relatedness, in accordance with demographic estimates of high levels of consanguineous marriage particularly in populations from the Middle East and central/South Asia, and it is similar to that observed for inbreeding-coefficient and identity-by-descent estimates. Third, in the admixed ASW and MXL individuals, total lengths of ROH in each size class are similar to those observed in populations from Africa and Europe, respectively (Figure 3).

“The total numbers of ROH per individual (Figure S4) show similar patterns to those observed for total lengths (Figure 3). However, in East Asian populations, total numbers of class B and class C ROH per individual are notably more variable across populations than are ROH total lengths.”

previously: runs of homozygosity and inbreeding (and outbreeding) and ibd and historic mating patterns in europe

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mating patterns in egypt

in family type in egypt, i hinted that inbreeding in egypt is greater in southern or upper egypt than in northern or lower egypt. now i’m going to show you the proof. PROOF i tell you! (^_^)

every few years, egypt conducts a demographic and health survey (so do a lot of other countries — thanks to us, i think). the egyptians, very thoughtfully, collect data on consanguineous mating patterns, i.e. first- and second-cousin marriages. here are the most recent egypt dhs surveys from 2000, 2005 and 2008 [all pdfs]. and here is a chart of the consanguineous (first- and second-cousin) marriage rates for four regions of egypt: urban governorates, lower egypt (delta) governorates, upper egypt (nile valley) governorates, and frontier (border regions) governorates (see list at bottom of post for which ones are which):

and here’s a map of those four regions:

the first thing you’ll notice is that egyptians marry their cousins a LOT. much more than americans or most europeans (esp. nw europeans). even in 2008, in cairo or alexandria nearly one in every four (23.2%) of all marriages were between people who were first- or second-cousins. and it was practically double that (41.2%) upriver in upper egypt. so, there’s a lot of cousin marriage in egypt — and much more in the south than in the north (told ya!)

the inbreeding rates have been decreasing over the last couple of decades, though. here is a chart of just the first-cousin marriage rates for pre-1991 (don’t ask me what that means – that’s all my source said), 1995, 2000, 2005 and 2008:

so, you know, just one generation ago, first-cousin marriage rates were twice as frequent in egypt as they are today. the decline is good news maybe, but keep in mind what the very recent high rates might mean for the frequencies and distribution of “genes for altruism” in the egyptian population. things don’t just change overnight.

father’s brother’s daughter (fbd) marriage is pretty popular in egypt. in 2008, nearly ten percent of all marriages were between the children of two brothers. there’s more fbd marriage in rural areas than in urban areas:

in Family in Contemporary Egypt [available on questia], andrea rugh says that the shift away from marrying cousins by urbanites began “about a generation ago.” rugh’s work was published in 1984, so she’s talking about sometime in the ’60s or maybe late-’50s. that means that nowadays there’s a good two or three generations of urban egyptians — not the recently arrived ones from the countryside, but people whose families have lived in the cities for several or maybe scores(!) of generations — that are now relatively outbred, certainly compared to most other people in the country. from rugh [pg. 140]:

“Among the middle classes and élites there is evidence that relative marriage persisted as a common form until the present generation of young people [i.e. in 1984 – hbd chick]. Until the 1952 revolution and the extension of education to the masses of Egypt’s population, there was little to interfere with the family as a key socializing institution. Those who received private educations did so in carefully sex-segregated institutions, along with their sisters or brothers, cousins, and well-screened others of the same social classes. Leisuretime socializing took place in the family courtyards or apartments of relatives. Parents exerted much stronger controls over whom their children met than they do now. Middle-aged and older people of those classes almost universally comment on how restricted their access to the opposite sex was, beyond those individuals of the extended family group with whom almost their whole time was spent.

Family genealogies of these classes are filled with kin and sibling marriages up until about a generation ago when, in an impressive reversal, stranger marriages replaced them in the vast majority of cases. This phenomenon to a large extent reflects the changing degree of parental control among these social classes. Young people now have greater freedom of movement, rationalized as noted by the increasing importance of extended education. Controls now are vested less in overt mechanisms such as confinement and protection (seen in chaperonage and veiling) and more in internalized ‘nice-girl’ constructs (see Chapter 9) which individuals implement to a large extent by themselves.”


rugh also found [pgs. 143-45] that father’s brother’s daughter marriage was more common amongst the lower classes in rural areas than urban areas. amongst the lower classes in urban areas, fbd marriage was still the most common form of cousin marriage, but mother’s sister’s marriage was also quite popular.

how long have egyptians been marrying their cousins or otherwise inbreeding or marrying endogamously?

well, certainly fbd marriage was most probably introduced when islam arrived in the country, i.e. from sometime after the seventh century a.d. so that’s, at the max, a possible 1600 years of fbd marriage — an interesting, quirky twist in history since that’s just about the length of time nw europeans have been outbreeding.

were egyptians inbreeding before that? hard to say. it seems like a good guess ’cause most peoples in the world have tended to inbreed one way or another. from the third century a.d. until the arrival of islam, most egyptians had been christians. but afaik, none of the christian churches started with this whole cousin marriage ban thing until the roman catholic church did in the 400s.

the ethiopian coptic ban on cousin marriage out to sixth cousins originated from something written by an egyptian copt in 1240 a.d. is that when egyptian copts began to avoid cousin marriage? if so, then they seem to have missed out on the roman catholic church’s revisions of its regulations in 1215 a.d. which pushed the ban from sixth cousins back to just third cousins.

on the other hand, perhaps the copts didn’t like that reversal and so in 1240 decided to re-emphasize their already existing sixth cousin ban. it’s possible. don’t know. just a guess. the timing seems awfully coincidental otherwise: 1215 a.d. -> changes in roman catholic church’s marriage regulations removing the sixth cousin marriage ban; a few years later in 1240 a.d. -> written proscriptions against sixth cousin marriage by the coptic church. hmmmm.

speaking of copts, i read something, somewhere that said that egyptian copts, today, prefer second-cousin marriage to first-cousin marriage, but i’ll be d*mned if i can remember where i read that. can’t find that reference, so don’t believe me! (i don’t.)

and i know what you’re gonna say: way back when egyptians married their siblings (ewwww!) just like the pharohs. actually, they probably didn’t. but that’s material for another post. this one’s way too long already anyway. (^_^)

previously: family type in egypt and corporations and collectivities and aígyptos

update 05/13: sounds to me as though, by the eleventh century a.d., copts in egypt had adopted the practice of marrying their cousins from their muslim overlords. at the very least, the coptic church at this time does not seem to have had a ban on cousin marriage.

here from “Regulating sex – A brief survey of medieval Copto-Arabic canons” in Across the Religious Divide – Women, Property, and Law in the Wider Mediterranean (ca. 1300-1800) [pgs. 29-30]:

“For Cyril [II] and Ibn Turayk, clergy are strictly forbidden from cohabiting with a woman, unless she falls under the category of one who is forbidden to him (muharrama). In his sixth canon, Cyril writes:

“‘It is not permitted to a bishop, or a priest, or deacon, or layman to live with a woman at all, unless it be a mother, or a sister, or a paternal aunt, or a maternal aunt who are forbidden to him. Whoever gainsay this, judgment for disobedience is necessary for him….’

“In the case of Cyril’s canon, it seems that no man (cleric or lay) should cohabit with a woman other than those ‘who are forbidden to him’ (tuharram ‘alayhi)….

“While there are parallels between both Cyril’s and Ibn Turayk’s canons and the Latern Council canon (which is actually a reference to a Nicene Council canon), there is also an important parallel between the Copto-Arabic canons and Islamic jurisprudential vocabulary. The Arabic words that Cyril and Ibn Turayk use to describe the category of forbidden women (Cyril uses form V’s tuharram a’layhi, and Ibn Turayk uses the plural passive participle muharramat) are borrowed from Islamic jurisprudence; the definition of this category may be understood from the Qur’anic verse found in Surat al-Nisa:

“‘Forbidden unto you are your mothers, and your daughters, and your sisters, and your father’s sisters, and your mother’s sisters, and your brother’s daughters and your sister’s daughters, and your foster-mothers, and your foster-sisters, and your mothers-in-law, and your step-daughters who are under your protection (born) of your women unto whom ye have gone in — but if ye have not gone in unto them, then it is no sin for you (to marry their daughters) — and the wives of your sons who (spring) from your own loins. And (it is forbidden unto you) that ye should have two sisters together, except what hath already happened (of that nature) in the past….'”

pope cyril ii was around from 1078-1092. his canon on which women were forbidden to men does not include any cousins, and it quite parallels what is written in the koran.

governorates breakdown:

urban governorates – cairo, alexandria, suez, port said.
lower egypt (delta) governorates – beheira, kafr el-sheikh, gharbia, monufia, damietta, dakahlia, sharqia, qalyubia, ismailia.
upper egypt (nile valley) governorates – giza, faiyum, beni suef, minya, asyut, sohag, qena, aswan.
frontier (border) governorates – matruh, new valley, north sinai, south sinai, red sea.

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more roh

in “Genomic Runs of Homozygosity Record Population History and Consanguinity” that i posted about yesterday, kirin, et. al., say:

“Europeans and East Asians have very similar ROH profiles in all but the shortest category (0.5-1 Mb). There are no significant differences between either the percentage of individuals with ROH of different lengths or sum length of ROH above different length thresholds (>1.5 Mb) for these two continental groupings (File S1). This is not surprising because both of these groups are mainly represented here by fairly large populations with no documented preference for consanguineous marriage.

ehhhhhhh … well … if they’re talking about now, i.e. in the present, then yeah — that’s probably pretty right. but many of the european populations that they looked at (i.e. from the human genome diversity project [hgdp]), regularly practiced some to quite a lot of consanguineous marriages up until fairly recently. (i haven’t checked into the asian populations that they looked at.)

the european populations that they looked at are: the adygeis, the basques, french folks, italians, orcadians, russians, sardinians and tuscans.

the adygeis are the circassians and it’s my understanding that they have avoided cousin marriage for quite some time, although they are endogamous (obviously). the russians — religious russians, anyway — avoid first- and second-cousin marriage. but the basques and the french have had some signficant amounts of consanguineous marriage up until quite recently. and the italians and sardinians?! holy toledo! of all of these groups, it’s probably the tuscans that have avoided cousin marriage for the longest. (dunno about the orkney islanders.)

like i said yesterday, if anything, kirin, et. al., have probably got some of the most inbred europeans in their sample.

anyway … i took at look at their supplemental info [opens pdf] and found that they’ve included data for the proportion (percentage) of the genomes from each group that are covered in “runs of homozygosity” (roh). the more roh in your — or your population’s — genome(s), the more inbred you (all) are (or maybe the smaller your gene pool is — see yesterday’s post). when i took out just the europeans plus the han chinese and japanese and a couple of other interesting groups, here’s what i got:

most of the european groups have the least number of roh (these are roh of all different lengths). the han chinese are like the italians or the sardinians, who have a long and recent history of close marriages (not so much the northern italians) — and the japanese even more so. wikipedia tells us that cousin marriage was preferred in china until the mid-twentieth century, so there you go.

and the father’s brother’s daughter’s marriage groups? their roh are higher than the inbred europeans, the han chinese and the japanese.

you can see here, too, that the japanese have greater numbers of longer roh than french people (the black circles are the japanese, the orange circles are the french) — that means more recent inbreeding amongst the japanese (click on image for LARGER view – should open in new tab/window):

interestingly, many balochis (green circles) have fewer and shorter roh than the french — many have more and longer. dunno what that tells us about the balochi. new blood? tribes merging with (fairly) unrelated tribes? just plain ol’ out-marriage?

here are the percentages of the genomes covered by roh for each of the populations in the study in ascending order. i tried to match the colors for the continental groupings from the chart in yesterday’s post — dunno if i succeeded?:

previously: runs of homozygosity and inbreeding (and outbreeding)

(note: comments do not require an email. balochi farmer. (^_^) )

baharnas and ajams and howalas, oh my!

so, tptb in bahrain are shooting @ the protestors:

Bahrain royal family orders army to turn on the people

“…Most of the protesters are members of Bahrain’s long-marginalised Shia majority.

“They say they are not demanding the abdication of Hamad bin Isa Al Khalifa, Bahrain’s Sunni king, but they are calling for a constitutional monarchy that would treat the Shia fairly and make them equal subjects in his kingdom.

“But they are demanding the resignation of his uncle Khalifa bin Sulman Al Khalifa, who has served as prime minister for 39 years.

“During his rule, the protesters say, the Shia have been turned into second class citizens, deprived of jobs in the army, police force and government while Sunnis from abroad have been given Bahraini citizenship to alter the kingdom’s demographic balance….”

“sunni” and “shia” are really just code words for a couple of populations of unrelated peoples that don’t get along.

in bahrain, the shia — who are probably 66% of the population — are the baharna, the arabs indigenous to the area. they happen to have as allies the ajam, some persians who settled in bahrain within the last 100 years.

i imagine that these two groups are allied together against the ruling “sunnis” just for convenience’s sake. they’d probably have a go at one another given the chance. kinda like how blacks and hispanics here in the u.s. are allied politically … for now ….

the sunni — who are probably 33% of the population — are in charge. they’re other arabs from an area in the center of the arabian peninsula. in other words, they’re really not related at all to the local baharna. they’ve been in bahrain for a couple of hundred years.

it’s kind-of like if the poles went and invaded and took over bulgaria. sure, they’re all slavs (arabs) so they’re related in one way, but clearly the poles (sunni arabs in bahrain) are not really bulgarians (baharna).


the king of bahrain, the prime minister, and roughly half of the cabinet are all members of the al khalifa clan, i.e. they’re all some of these non-bahraini arabs from central arabia.

allied with these sunni arabs that are in charge are the huwala, who were a bunch of sunni arabs from a bunch of different areas who migrated to persia at one time but then came back to the arabian peninsula. (there’s some persians mixed into that group just to add to the confusion.) and, also, the descedants of the african slaves that had belonged to the al khalifas once-upon-a-time are allied to them. oh, there’s also some bedouin tribes in bahrain that are allied to the sunnis in charge.

so, there’s the “bahrainis for dummies” breakdown for you, as far as i understand it.

don’t let THEM throw you off with all this “sunni”/”shia” nonsense. religion and religious sects ain’t got nothing to do with it. not ultimately anyway. there’s a minority of foreigners (+ their allies) ruling over a majority of natives (+ their allies), and the natives are a little fed up, especially since the rulers have been busy electing a new people.

oh, and yes the clans in bahrain inbreed, too. the first- plus second-cousin marriage rate in 1989 was 31.8%.

previously: cousin marriage conundrum addendum and aígyptos

update: from The Menas Associates Blog

“During the 1990s, there were several years of Shi’a rioting and low level violence mostly in rural areas against a constitution that allowed them virtually no representation. When King Hamad took power in 1999 he offered a new deal whereby the Shi’a appeared to be able to vote freely for a Lower House which would have the main say in parliament. He later altered this to an equal voice to the Upper House. Election arrangements for the Lower House are organised (i.e. gerrymandered) to ensure that the Shi’a are under-represented….

“There are also strong suspicions that the regime has been granting nationality to Sunni from Jordan and other countries in an effort to increase Sunni demographic size…..”

update 02/21: see also steve sailer’s Bahrain—Electing A New People…And Shooting The Old One

update 02/22: see also IAmA Bahraini Citizen, and I will tell you what’s REALLY going on in Bahrain.

update 03/11: from“The way that government officials are appointed reflects the importance of tribal connections. Members of the ruling family are accommodated first, followed by families and tribes with whom the rulers have been traditionally allied. In Bahrain, for example, the ruling Al Khalifa have given the major positions in the bureaucracy to Sunni Arabs from tribes that helped them rule the island in the nineteenth century. The Al Khalifa have given lesser positions to Shia Arabs from merchant families with whom they engaged in the pearl industry but with whom they had no tribal alliances. But the Al Khalifa have been reluctant to give positions of authority to Shia farmers of Iranian descent to whom they had neither tribal nor economic ties.”

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