so why DID the japanese quit marrying their cousins?

one of the reasons seems to have been that the policy was, indeed, part of the modernization/westernization move in late-nineteenth century japan (sort-of the opposite of what happened in the maghreb/mashriq/parts of south asia when they went through an arabization process — oops! — bad luck).

from “Japan’s Outcaste Abolition: The struggle for national inclusion and the making of the modern state” [pgs. 82-83] (the “new commoners” referred to here are the burakumin whose social status changed with the “edict abolishing ignoble classes” — they were literally new commoners after moving up in the world [theoretically anyway]. “eta” also=burakumin. links added by me.):

“[O]ne of the main government aims of the time was to improve the national stock so as to maximize economic productivity and military power, as expressed in the slogan ‘rich country, strong military’. Although eugenics as a scientific discipline was not introduced into Japan until the end of the Meiji period, the Meiji government had from its inception followed policies to foster stronger and healthier Japanese bodies through its encouragement of milk-drinking and meat-eating, as well as through its public hygiene and health policies. If there was a hereditary and inferior Eta nature that was biologically transmitted, then it would be in the national interest to minimize relationships between New Commoners and others.

“The leaders of the semi-official Greater Japan Private Hygiene Association, whose purpose was to improve the nation’s human resources and to heighten people’s value as labour and military power, made explicit this connection between state interests and individual health. At this body’s inaugural assembly in 1883, its president and the future head of the Japanese Red Cross, Sano Tsunetami (1822-1902), declared that, ‘the health of each of us is related to whether our country shall be strong or weak, rich or poor’. Another executive, the medical doctor Hasegawa Yasushi (1842-1912), pronounced that the association’s aim was to ‘make the nation healthy, foster the strength that is the font of capital, [...] and thereby increase militarisation’.

“Intellectuals debated precisely how the state might realize the goal of improving its human resources. Based on notions of a racial hierarchy topped by Westerners, holders of one extreme view proposed that Japanese people should interbreed with Western people. ‘The physiques and minds of Japanese are inferior to Westerners’, one writer argued, going on to propose that ‘we should import [Western] women…”

heh! (~_^)

“…and promote meat-eating to further improve our race’. While the latter idea about eating more meat proved popular, the former proved contentious. Hozumi Yatsuka attacked plans for racial interbreeding on the grounds it would adversely affect ancestor worship, a practice that in his opinion underpinned the Japanese nation.

“In somewhat more scientific fashion, the pre-eminent conservative intellectual Kato Hiroyuki pointed out in 1887 that if Westerners were racially superior and their genes dominant, then rather than improving the Japanese race, intermarriage between Western women and Japanese men would lead logically and unacceptably to the eventual replacement and disappearance of Japanese. Partly as a result of such criticisms, Japanese scholars ‘tended to emphasise environmental elements over genetics’, and devised practical plans to improve the population by reforming and improving people’s lifestyles.

“People who looked at ways to reform popular lifestyles from the perspectives of national health and state power turned their attention to improving sanitation and diet and also drew attention to the problem of ‘inbreeding’ or marriages between close blood relatives. They considered inbreeding practices to be widespread, and thus to pose a serious problem, since they gave rise to disease and deformity, and ultimately would bring about ‘racial decline’. In light of these unwanted effects, intellectuals and officials called on people to desist from such unions.

“There had been occasional attacks on inbreeding during the early Meiji years. In 1875, Minoura Katsundo (1854-1929), a student of Fukuzawa Yukichi, had bemoaned the fact that alliances between close blood relatives were causing aristocratic degeneracy. Such claims were countered, however, by arguments that inbreeding was necessary to maintain the purity of aristocratic bloodlines. But growing out of a more general concern with ‘racial improvement’ among the socio-political elite, the concern with inbreeding that emerged in the latter part of the Meiji period was much broader in its focus, and it was given legal grounding by the 1898 Civil Code, which prohibited marriages between close relatives.“

my questions are: first, what does “close relatives” mean? presumably first cousins anyway. then, how well was this civil code enforced? or was it changed at some point? or did the japanese not have to register their marriages with the state? or were there a lot of exemptions or something? because if there was a law banning cousin marriage in japan, why then were 22.4% of marriages in japan in the 1910s-1920s between cousins? (i actually saw a figure of 50% in something i was reading yesterday — need to find it again.) lots of looking the other way by officials? bribery? what was going on?

more from the book:

“A noteworthy aspect of the mid-to-late-Meiji anti-inbreeding campaign was that writers alleged that practice to be prevalent among New Commoners. Their claims may have had the effect of discouraging some people from inbreeding practices, as presumably the threat of becoming alike to New Commoners constituted a powerful disincentive. Such claims may have had some basis in the fact that discrimination limited the marriage pool of New Commoners and thus promoted community endogamy. But to target New Commoners as particular practitioners of this ‘offence’ was to ignore the fact that marriage relations between close relatives were not all uncommon among the population generally, and were prevalent especially among the upper reaches of society.”

previously: japan – reversal of fortune? and historic mating patterns in japan

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japan – reversal of fortune?

a couple of months ago, greg cochran wrote about how a population (any given population) might raise its average iq quickly — like over two or three generations. one possible method, he suggested, was to quit inbreeding. here’s what he said:

“I’ve been thinking, off and on, about sudden changes in the cognitive abilities of populations: groups low suddenly scoring much higher or lower on a time scale too short to be explained by selection: say, three generations or less…. I can think of two perfectly feasible strategies that *would* cause significant one-generation increases in intelligence, in certain populations. Iodine supplementation, in places where it’s short, has a big payoff…. The other practical, low-tech strategy would be stopping cousin marriage. The next generation would be in much better shape, since the children of first cousins take a substantial IQ hit – maybe six points or so.“

i think i may have stumbled across an example of a population rapidly dropping cousin marriage and, also very rapidly, gaining iq points.

japan.

yesterday, i was working on a completely different post about japan and cousin marriage, when i rediscovered this [pg. 30] (click on chart for LARGER version):

that’s the decline in the average national consanguinity rates in japan from 1947 to the early-1980s. but the consang rates were even higher in the 1910s-1920s at 22.4% [pg. 29] (and who knows how high the rates might’ve been even further back?), so the chart above should look something more like this (pardon my crayola — and note that i just eyeballed it — click on chart for LARGER version):

when i rediscovered this yesterday, i remembered what greg had written, and got to wondering if there were any historic data for japanese iqs and if there’d been any changes in those iqs over time. so i googled (as one does) … and found this:

The Rise of National Intelligence: Evidence from Britain, Japan and the U.S.A. [pdf] – lynn and hampson.

from that article [pgs. 27-31]:

“It has been possible to find five studies providing evidence on the secular trend of intelligence in Japan for the post World War II period….

“(1) Ushijima’s study (1961)….

“Here the Ushijima intelligence test was administered to 1365 children in 1953 and to a comparable sample of 1370 children in 1960 with the objective of determining any change in the mean over this relatively short period. The children were aged 9-15 years.

“(i) All age groups show a rise in scores for all abilities. The overall mean increase was 0.66 standard deviations, the equivalent of 9.9 IQ points, and representing an IQ gain of 14.1 IQ points per decade. This is of course a very considerable increase and much greater than anything found in either Britain or the U.S.A.

“(ii) The IQ increases are in general greater among the younger age groups than among the older….”

see my crayola chart above. kids who were fifteen in 1953 would’ve been born way back in 1938 when the consang rates were above 15% — maybe 17 or 18% (remember, i just eyeballed it, so this is a complete guess really) — while kids who were nine in 1953 would’ve been born in 1944 when consang rates were hovering right around 15%, in other words lower. same for the later cohort from 1960: fifteen year olds would’ve been born in 1945, nine years old in 1951. the younger the kids in the cohorts, the less chances their parents were related.

more from the article…

“(2) Kaneko’s study (1970)….

“Kaneko’s invetigation of a possible rise in the scores on this test was carried out in 1963….

“Hence the mean IQ in these schools has risen 10.38 IQ points over the 9-yr period … represents an IQ gain of 11.4 IQ points per decade. This figure is evidently broadly similar to the rise of 14.1 IQ points per decade for 1953-1960 found by Ushijima and confirms a very considerable rate of IQ gain in Japan in these early post World War II years.

“(3) Sano’s study (1974)….

“It will be seen that in all samples there were considerable increases in mean IQ from 1954 to 1972. The increases appear to be a little greater among the city children than among those from the prefrecture. When the results for 10- and 11-yr olds are combined, city children gained 18.04 IQ points and prefrecture children 15.07 IQ points….”

that the city children had greater gains than the rural kids is not surprising if inbreeding is the factor making the difference here. even up to the 1980s, consanguinity rates have been quite a bit lower in urban areas in japan as compared to rural areas (see table in this post for example). (more on this soon in that upcoming post on japan.)

“The average of the two gains is 16.56 IQ points, representing a gain of approx. 9.15 IQ points per decade for the entire sample.

“Sano also considered the question of whether the IQ gains in Japan have been increasing at a constant rate. For this he used Kaneko’s 1964 data which were available for two of the schools. He calculated that the increase in mean IQ was 10.47 points for 1954-1963 and 3.42 for 1963-1972…. ([I]t will also be noted that the gain of 10.47 IQ points for 1954-1963 is closely similar to Kaneko’s figure of 10.38 for the same period.)

“It is apparent therefore that there was a considerable deceleration in the rate of increase in intelligence over the period 1954-1972….”

again, see my crayola chart. the decline in cousin marriage rates is much sharper in the decades preceding 1954 than during those preceding 1963. in other words, there was a deceleration in the reduction of cousin marriages over time, so perhaps we shouldn’t be surprised at a deceleration in the increases in iq over time.

“(4) Wechsler studies….

“Thus after making these adjustments we have Japanese mean IQs of 101.9 for 1951 and 107.4 for 1975. Hence over this 24-yr period (1951-1975) the Japanese mean IQ increased by 5.5 IQ points relative to the American IQ…. This represents a Japanese IQ gain of 5.75 IQ points per decade. This rate of increase for the period of 1951-1975 is somewhat less than Sano’s result of a 9.15 IQ point per decade increase over approximately the same period (1954-1972)….

“A second Japanese study using the WISC and WISC-R is also available (Anon, 1981)…. This gives a rise of 20.03 IQ points over the 24-yr period, making 8.34 IQ points per decade….”

lynn and hampson conclude:

“The conclusion of the Japanese studies is as follows. Two studies of the early post World War II period show substantial IQ gains of 9.9 and 11.4 IQ points per decade. Three studies of a longer period from approx. 1950-1975 show lower IQ gains of 9.1, 8.3 and 5.7 IQ points per decade, giving an average gain of 7.7 IQ points per decade. Since the early part of this period was characterized by a greater rate of gain, it appears that since around 1960 the IQ gains in Japan have decelerated to approx. 5 IQ points per decade….

“It is not particularly surprising that the Japanese gains should have been the greatest of the three countries. Japan was a relatively underdeveloped country in the 1930s with a per capita income about one eighth of that of the U.S.A.”

but the country was probably relatively underdeveloped because the japanese had a lower average iq at the time, and it’s since increased phenomenally … due to the sharp and rapid decline in inbreeding in japan? and so has their economic success obviously.
_____

i’d be curious to know two things:

- why did the japanese quit marrying their cousins? was there some official policy out there discouraging it — as part of their general modernization, “be more like the westerners” move? did the people just naturally adopt it as part of that westernization package? was it connected to christianity in japan? (japanese catholics historically had lower first cousin marriage rates than other religious groups — i’ll get to this in my upcoming post on japanese cousin marriage — the one that i was working on yesterday!). was it related to industrialization and urbanization? all of the above? none of the above?

- has something similar happened in china and/or korea (or elsewhere for that matter — i mean in modern times)? the cousin marriage rates for china are reportedly very low — today — but i’m pretty sure they were much higher in the past — even the recent past (see mating patterns in asia series below ↓ in the left-hand column), but i don’t have as good data for china as what i’ve presented here for japan. but inquiring minds want to know!

see also: Reversal of Fortune

previously: historic mating patterns in japan

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linkfest – 12/16/12

Finland & Japan – exceptions to “the rule”? – from jayman!

Genetic pacification in medieval Europe – from peter frost!

Scientists May Have Finally Unlocked Puzzle of Why People Are Gay – an epigenetic cause of gayness?

Restless Genes – drd4.

Reconstructed Face of Extinct “Hobbit” Species Is Startlingly Humanlike

Polymorphisms and Load – (more stuff i barely understand) from greg cochran!

Penn Study shows resistance to cocaine addiction may be passed down from father to son – in rats anyway.

Where to be born vs. where people are being born – from the awesome epigone!

The mu opioid receptor genotype may be a marker for those who drink for alcohol’s rewarding effects – OPRM1.

bonus: Lead poisoning in Samurai kids linked to mom’s makeup

bonus bonus: OU Study Suggests the Bacterial Ecology That Lives on Humans Has Changed Dramatically in the Last 100 Years

bonus bonus bonus: Microbiome: Cultural differences – “Studies of gut bacteria are beginning to untangle how diet affects health in old age — but determining cause and effect is tricky.”

bonus bonus bonus bonus: Art of cheese-making is 7,500 years old

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historic mating patterns in japan

readers (luke & jayman) request: what about the japanese? well, we aim to please… (^_^)

the japanese definitely have a history of cousin and endogamous marriages. i’m not sure, yet, how far back it goes (although i’m going to guess pretty d*rn far), but between 1912 and 1925 the consanguinity (first-/second-cousin) marriage rate for japan was 22.4% [pg. 29]. compare that to italy toward the beginning of the twentieth century or to some of the arab countries today. compare it also to the first cousin marriage rate amongst rural english folks in the 1870s: 2.25% (4.5% for the peerage).

but it’s been decreasing ever since (looks like a stock market crash – pg. 30):

by wwii the rate was only about 12.3%, and nowadays it’s like 4% (3.9% in 1983).

imaizumi, the author of the article to which i’ve linked above, also found in the early 1980s that 27% of recently married japanese folks had married endogamously, while amongst the oldest folks studied, 40% had married endogamously [pg. 39]. so endogamous marriages have also declined in japan over the course of the twentieth century. still, more than 1 in 4 japanese entered into an endogamous marriage in the ’80s (or maybe the late 1970s).

seems like the shintoists practice cousin marriage most frequently, followed by buddhists, and is lowest amongst catholics. farmers/fishermen, blue collar workers, the self-employed and people working in services (like transportation) inbreed the most, whereas white collar workers, salesmen and professionals inbreed the least.

note: the type of cousin marriage practiced in japan is mostly mother’s brother’s daughter (mbd) marriage as in china. more on that in the next post on japan. that’s important because mbd marriage amounts to less inbreeding (i think) than the arab type of cousin marriage (father’s brother daughter or fbd marriage) since all of the marriages do NOT occur exclusively in one lineage. in mbd marriage, at least more than one other lineage is involved.

the events of the meiji period obviously shook up the social structures in japan a LOT, but i wonder if cousin marriage/endogamy was officially — or even unofficially — discouraged in any way during that time period. i’m wondering if what happened in europe starting in the early medieval period regarding mating patterns has sorta been repeated in japan, only starting in the nineteenth century. -?-

goes to show, too, how rapidly cousin marriage rates can drop — within one generation in japan cousin marriage rates halved. maybe this could happen only amongst east asians who are big into conformity, but it’s something to keep in mind when trying to imagine what happened in europe in the medieval period, i.e. that things could’ve moved pretty quickly.

more anon!

previously: on the non-violent japanese of today

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linkfest – 05/13/12

China: The world’s cleverest country? – “China’s results in international education tests – which have never been published – are ‘remarkable’, says Andreas Schleicher, responsible for the highly-influential Pisa tests.”

Dumb and Dumber – yeah, that was pretty dumb alright. steve sailer explained all the ways why.

Science Reveals Why We Brag So Much – “Talking about ourselves—whether in a personal conversation or through social media sites like Facebook and Twitter—triggers the same sensation of pleasure in the brain as food or money, researchers reported Monday.”

Infant testosterone predicts toddler behavior – from the inductivist.

Study finds psychopaths have distinct brain structure – “The study showed that psychopaths, who are characterized by a lack of empathy, had less grey matter in the areas of the brain important for understanding other peoples’ emotions.”

Religious conservatives in the U.S. more liberal than the Muslim masses are – from the audacious one.

Neighboring chimp communities have their own nut-cracking styles

Dopamine Distribution Causes Slackers And Go-Getters? – from parapundit.

bonus: Falling birth rates mean Japan ‘won’t have any children under 15 by 3011′ – sounds more impending when they put it that way, doesn’t it? =/

bonus bonus: The Mysterious Case of the Vanishing Genius – about margie profet.

bonus bonus bonus: Is Einstein’s Greatest Work All Wrong—Because He Didn’t Go Far Enough?

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more on the hgdp samples

first, see my previous post on this if you want to follow along.

in that post, i expressed some concerns over the french human genome diversity project (hgdp) samples since the ceph folks describe them as: French (various regions) relatives. i wondered both of the following: 1) how many and which “various regions,” since different regions of france have historically had different rates of inbreeding — haven’t managed to find out which “various regions” — and 2) how many and what sorts of relatives? i did find out that.

via some genetic wizardry, a noah rosenberg tried to work out if any of the individuals in any the hgdp samples were, in fact, relatives [see here]. to cut a long story short, rosenberg found it likely that two individuals in the french sample were siblings [see pg. 7 here - opens pdf], thus the “relatives” indicator on the ceph website. so, the entire french sample is NOT full of family members like i wondered in my last post — only two of the individuals sampled are likely to have been relatives.

i still think it would be useful to know from which regions the samples were drawn, but i guess i just have to live with not knowing for the meantime. (~_^) but now i feel more secure about professor harpending’s conclusion — that regarding the french: “from the viewpoint of kinship, one person is not very different from another person.”

however, now i feel unsure about the japanese samples! the hgdp samples for the japanese are described on ALFRED as:

“Collected by L.L. Cavalli-Sforza from Japanese-born individuals living in the San Francisco Bay area, and by K.K. Kidd and J. R. Kidd from Japanese-born individuals living in Connecticut.”

ack! well, how representative of japanese people in japan are these people? where did they come from? urban areas? rural areas? different areas? mostly the same areas? how old were they?

i ask all these questions because, historically, urban japanese have had lower inbreeding rates than rural japanese … and the inbreeding rates overall for japan dropped pretty sharply after wwii [see pgs. 4-5 here - opens pdf]. so if the samples include mostly young, urban japanese who recently moved to the u.s., well i wouldn’t be surprised if they look quite outbred. but if the samples include mostly older, rural japanese, i would be surprised if they looked outbred.

now i don’t have any confidence in the japanese hgdp samples — not for looking at kinship within the japanese population anyway. btw, rosenberg didn’t find any likely relatives in the japanese samples.
_____

i went through the ceph table of the hgdp samples and ALFRED and compiled a list of all the hgdp samples and if they 1) likely include any family members (“relatives” – based on rosenberg), and 2) where the samples were collected and from whom, if known. many of the samples don’t have any useful information on their provenance. for example, many of the ALFRED entries say that the samples were drawn from unrelated individuals, but rosenberg found that they, in fact, likely included relatives.

why do i care about any of this? i’ll explain that in another post. right now … coffee! (^_^)

**update: see why i care about the hgdp samples**
_____

the list:

- Central African Republic – Biaka Pygmy (relatives)
This sample is comprised of Biaka, living in the village of Bagandu, in the southwest corner of the Central African Republic (3.42N; 18E altitude approximately 500m). This group is probably an admixture of 3/4 “non-pygmy” African ancestry and 1/4 Mbuti ancestry. The transformed cell lines were established by Judith R. Kidd. The sources of this sample are L. Cavalli-Sforza (Stanford University) and K.K. Kidd, J.R. Kidd (Yale University).

- Democratic Rep of Congo – Mbuti Pygmy (relatives)
The sample is composed of Nilosaharan and Niger Kordofanian speaking Mbuti pygmies from the northeastern part of the Ituri Forest (northeastern Democratic Republic of the Congo). It was collected by L.L. Cavalli-Sforza in 1986.

- Senegal – Mandenka (relatives)
This sample from the Central African Republic is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Nigeria – Yoruba (relatives)
Most of the Yoruba individuals in this sample are urban health care workers from Benin City, Nigeria, collected by Prof. Friday E. Okonofua and collaborators; cell lines established by Dr. J.R. Kidd.

- Namibia – San (relatives)
This sample from Namibia is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Kenya – Bantu NE (relatives)
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- S. Africa – Bantu SE Pedi
- S. Africa – Bantu SE Sotho
- S. Africa – Bantu SE Tswana
- S. Africa – Bantu SE Zulu
- S. Africa – Bantu SW Herero
- S. Africa – Bantu SW Ovambo
These samples are part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). They include the following individuals: #993, 994, 1028, 1030, 1031, 1033, 1034, and 1035. These samples consist of unrelated Bantu speakers from southern Africa and were collected with proper informed consent.

- Algeria – Mozabite (relatives)
This sample from Algeria is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Israel (Negev) – Bedouin (relatives)
This sample from the Negev region of Israel is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Israel (Carmel) – Druze (relatives)
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). The Druze, a Moslem community from Northern Israel. Collected by B. Bonne-Tamir (Tel Aviv University) as part of the repository of samples of Israeli populations. This sample contains both related and unrelated individuals.

- Israel (Central) – Palestinian (relatives)
This sample from the central region of Israel is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Pakistan – Brahui
- Pakistan – Balochi (relatives)
- Pakistan – Hazara (relatives)
- Pakistan – Sindhi (relatives)
- Pakistan – Pathan
- Pakistan – Kalash (relatives)
- Pakistan – Burusho
These samples from Pakistan are part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). These samples consist of unrelated individuals and were collected with proper informed consent.

- Pakistan – Makrani
*no info found.*

- China – Han
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This is a sample of Han Chinese living in the San Francisco, California. Collected by L. Cavalli-Sforza (Stanford University), K.K. Kidd, and J.R. Kidd.

- China – Tujia
- China – Yizu/Yi
- China – Miaozu/Miao
- China – Oroqen (relatives)
- China – Daur
- China – Mongola
- China – Hezhen
- China – Xibo
- China – Uygur
- China – Dai
- China – She
- China – Lahu (relatives)
- China – Naxi (relatives)
- China – Tu
These samples from China are part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). These samples consist of unrelated individuals and were collected with proper informed consent.

- Siberia – Yakut
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). Yakut-speaking individuals in the Yakut Autonomous Republic. Individuals sampled were living or were born along the river Lena in the area of Yakutsk and northward, roughly 129-130E, 62-64N. This sample was collected by E.L. Grigorenko.

- Japan – Japanese
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). Collected by L.L. Cavalli-Sforza from Japanese-born individuals living in the San Francisco Bay area, and by K.K. Kidd and J. R. Kidd from Japanese-born individuals living in Connecticut.

- Cambodia – Cambodian (relatives)
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). Collected by K. Dumars from individuals born in Cambodia who are now living in Santa Ana, California.

- France – French/various regions (relatives)
This sample form various regions of France is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- France – Basque
This sample from France is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Italy – Sardinian
This sample from Italy is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Italy – from Bergamo
- Italy – Tuscany
*no info found.*

- Orkney Islands – Orcadian (relatives)
This sample from the Orkney Islands is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

- Russia Caucasus – Adygei
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). Adygei-speaking people near Krasnodar in the Russian republic of Adygei, which is in the southeastern section of the country (north of the Caucuses mountains). They are culturally and linguistically distinct from neighboring Russians. This sample was collected by E. Grigorenko (Yale University) V. Galkina, and M. Kadoshnikova (Bristol company, Russia).

- Russia – Russian
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). Sample collected by E. Grigorenko from rural communities of ethnic Russians living in the Vologda Administrative Region, about 400 km north of Moscow, roughly 59-61N, 39-41E.

- Mexico – Pima (relatives)
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). Collected from Pima living near the eastern border of the state of Sonora, Mexico. Collected by L.O. Shulz.

- Mexico – Maya (relatives)
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of Mayans who are Yucatec speakers from in the Xmaben village located in the Mexican state of Campeche in the central Yucatan peninsula. Blood and serum markers indicate European admixture to be about 10 % (K. Weiss, personal communication). Some evidence suggests that the area from which this sample was drawn served as a refuge for Maya people from across southern Mexico who fled to this more remote region during a series of revolts against the Spanish in the 19th and early 20th centuries. There are 53 transformed cell lines (106 chromosomes) established by Judith R. Kidd. The sources of this sample are K.K. Kidd and J.R. Kidd (Yale University).

- Colombia – Piapoco and Curripaco (relatives)
*no info found.*

- Brazil – Karitiana (relatives)
This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). The sample was collected in the Karitiana village (Rondonia Province, Brazil) by F. Black. HLA haplotypes indicate that the Karitiana have no non-Amerindian admixture and are genetically distinct from other sampled populations in relative geographical proximity, such as the Surui.

- Brazil – Burui (relatives)
*no info found.*

previously: hgdp samples and relatedness

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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.**
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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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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)

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