russians, eastern europeans, runs of homozygosity (roh), and inbreeding

greying wanderer (thanks, grey!) pointed out to me (via) a very interesting study of russian/eastern european genetics which includes some runs of homozygosity (roh) data (which can provide clues of inbreeding/close matings among other things): A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe. (dienekes has a really good explanation of roh here.)

in this latest study, khrunin et al. took a look at a handful of different ethnic russian sub-populations (from different locations in russia) as well as some other eastern european groups. most of the samples from russia they collected themselves — the rest came from other studies. here’s a list of which groups were included and where they came from:

- russians (n=384) from the archangelsk (mezen district, n = 96), vladimir (murom district, n = 96), kursk (kursk and oktyabrsky districts, n = 96), and tver (andreapol district, n = 96) regions
- veps (n=81) from the babaevo district of the vologodsky region
- komi (n=150) from the izhemski (izhemski komi, n = 79) and priluzski (priluzski komi, n = 71) districts of the komi republic.

all of these samples were collected by the authors — except for those from tver — and the researchers ensured that the subjects AND their parents were originally from whatever region in which they happened to find them (i like that!).

the data from other studies which they used are described in this paper and include:

- finns – samples from helsinki (n = 100) and kuusamo (n = 84) – kuusamo is really remote
- estonians (n = 100) – samples collected across the entire country
- latvians (n = 95) – samples collected in riga – parents had to be latvians
- poles (n = 48) – from the west-pomeranian region, so just on the border with germany
- czechs (n = 94) – from prague, moravia, and silesia
- germans (n = 100) – from schleswig-holstein in the north and the augsburg region in the south
- italians (n = 88) from tuscany – hapmap
- russians (n = 25) from the human genome diversity panel (hgdp) – i believe from the vologda oblast.

the data collected by khrunin et al. are really good, imho, since 1) they went to all the trouble of collecting samples from different regions of russia, and 2) the researchers tried to control for ethnic/regional origin. the quality of the data from all the other studies is kinda mixed, for my interests anyway. for instance, taking in samples in large, capital cities — meh — not so great. the residents of those cities could’ve come from all over the country. the northern versus southern sampling in germany is better; unfortunately, those data sets were combined together in this study (they’re kept separate in another really cool study which i will post about soon!). the estonian data set is interesting because the samples came from across the country. otoh, the polish data set is also interesting because it’s from such a specific region (and right on the border with germany).

ok. one last thing before i show you the results (i made a map!). different researchers define roh differently (*sigh*) — while there do seem to be some standards, there’s also quite a bit of variation, and different researchers choose to look for roh of varying lengths. in this study, the researchers looked for roh that were 1.5Mb in length (i’ve seen other researchers look for 1Mb in length). 1.5Mb is pretty short as far as roh go. if you recall, when a population has a lot of longer roh (like 4-8Mb or more), that’s a pretty good indicator of inbreeding. 1.5Mb — not so much. lots of short roh are a better indicator of something like a population bottleneck in the distant-ish past. but, what’s a girl to do? gotta work with what’s available, and if it’s short roh, so be it.

here (finally!) is the map. i took the data from this table. the map (first column of data) is of the average number of roh (of 1.5Mb) found in individuals in the different populations (nROH):

the most obvious thing to note is that the small, endogamous groups (the veps and the komi) have more roh than any of the other populations, except for the finns up in kuusamo (and i think that that’s probably due to a bottleneck — ethnic finns really only migrated to, and began to settle in, the area seriously in the 1600s, and i imagine it wasn’t very many of them — and being so far away from anybody else!). the veps and the komi are small populations and, historically, they didn’t marry out much (that’s why we have veps and komi people today), so they are somewhat inbred. definitely more so than the surrounding population.

another curious thing is the pretty high number of rohs in the baltic populations: latvians=0.58, estonians=0.61, and finns in helsinki=1.13. wow! what happened there? that’s something like three to five times the number of roh we see in italians (from tuscany) or germans.

the most interesting point for me, though, is that there is an east-west divide. it’s kinda vague, maybe, but i think it’s there: italians (tuscans) and germans at ca. 0.20, and then the czechs and poles right next door at 0.35 and 0.51 respectively. and everyone to the east, except the russians in kursk, higher again than those two figures. i think these results hint at what i’ve found in the history books on medieval europe, i.e. that western europeans began outbreeding earlier than eastern europeans and as a result wound up being more outbred. (see, for example, here and here — and the “mating patterns in europe series” below ↓ in left-hand column.)

finally, the authors of the study point out how it appears that the average number of roh in individuals in a population increases with latitude — and they mention that this has also been shown elsewhere (i’ll be posting on that paper — very soon!). if you look at the various ethnic russian populations, for instance, the russians down in kursk (Rus_Ku=0.28) and murom (Rus_Mu=0.39) have fewer roh than the russians further to the north in tver (Rus_Tv=0.49) and way up in mezen (Rus_Me=1.63!). however, the hgdp russian samples, apparently from the vologda oblast which is pretty far north, have relatively low numbers of roh (Rus_HGDP=0.44), so that doesn’t seem to fit. still, it does look like a real pattern to me. the authors suggest that this is due to the general pattern of how europe was settled (from the south to the north), as well as the fact that the farther north you go, the fewer people there are to mate with (so the more inbred you wind up being).

as i’ll show in my next post, though, while there does seem to be a north-south pattern to roh frequency in europe with more roh in populations to the north than the south, curiously the numbers seem to increase in southern europe as well (as compared to places in central europe like germany and france) — and strangely in the balkan region as well. i can’t imagine why! (^_^)

previously: ibd and historic mating patterns in europe and ibd rates for europe and the hajnal line and runs of homozygosity and inbreeding (and outbreeding) and runs of homozygosity again

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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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linkfest – 09/09/12

Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role – “As scientists delved into the ‘junk’ — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed. The result of the work is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.”

New Research Suggests Bacteria Are Social Microorganisms – “The research shows that a few individuals in groups of closely related bacteria have the ability to produce chemical compounds that kill or slow the growth of other populations of bacteria in the environment, but not harm their own.” – cooooooool!

Further Testing the Pioneer Hypothesis: Canada and Russia – from jayman.

Racial and ethnic diversity spreads across the country – “Another significant finding is the decline in white-dominant places, where whites make up 90 percent or more of the population. Three decades ago these places represented two-thirds of the total. Today, they are down to only one-third of the total. In their stead are a growing number of communities where minorities are a significant share of the population and often where no group is a majority.” – see also nowhere to run.

Finnish ancestors’ diet explains many modern ailments – finnish cannibals!! also: “The late arrival of agriculture in Finland is still reflected in the Finnish people. According to Markku Niskanen a researcher into archaeology at the University of Oulu, the Finnish genotype is still not adapted well to the food that was introduced through agriculture, to say nothing of industrially produced nutrition. Niskanen believes that a possible reason why we have more adult-onset diabetes than other Europeans is that we are not accustomed to eating large amounts of grain.”

Social psychologists espouse tolerance and diversity — do they walk the walk? – see also Survey finds blatant bias and discrimination against conservatives in academia.

Redebunking Ron – chuck has “marshaled evidence from no less than 14 nationally representative samples (PISA 2009, PISA 2006, TIMSS 2007, PIRLS 2006, PIRLS 2001, ADD Health, GSS, NLSY 79, NLSY 97, CNLSY, NAEP Main, NAEP Long term, High School Transcript Study, and NELS) and demonstrated beyond a doubt that the claimed Ron effect was a mirage.”

bonus: Species multiply as Earth heats up – “[E]ras of warming were accompanied by increases in biodiversity.” – previously evolution likes it hot.

bonus bonus: Evolution could explain the placebo effect — “The model revealed that, in challenging environments, animals lived longer and sired more offspring if they endured infections without mounting an immune response. In more favourable environments, it was best for animals to mount an immune response and return to health as quickly as possible.”

bonus bonus bonus: The birdy smell of a compatible partner – “New evidence shows that birds may choose their mate with the help of smell. They prefer a dissimilar mate because this gives their young a more efficient immune system.”

bonus bonus bonus bonus: Ancient, bottom-dwelling critter proves: Newer isn’t always better – “Tiny, humble rhabdopleurids have lived on the ocean floor for some 500 million years, outlasting more elaborate descendants”

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mitä kuuluu suomalaisten kanssa?

oh, no! finns in finland have a shorter life-expectancy than swedes in finland. ‘sup with that? (these researchers think it could be something genetic.):

“Family origin and mortality: prospective Finnish cohort study”

“Background: Death rates are notably higher in eastern Finland than in western Finland, and life expectancy of Finnish speakers shorter than that of Swedish speakers. The mortality differences correspond to recent genetic mappings of the population and are prominent for causes of death that are known to be associated with genetic risk factors….

“Result: The death risk of Finnish speakers born in eastern Finland was 1.13 (95% confidence interval 1.01 to 1.26) that of Finnish speakers born in western Finland, whereas that of Swedish speakers was only 0.60 (0.52 to 0.71). In Finnish speakers, the effects of own birth area and area of residence disappeared when parental birth area was accounted for. The death risk of persons with at least one parent born in eastern Finland was 1.23 (1.09 to 1.39) that of people with both parents born in western Finland.

“Conclusions: Parental birth area is the driving force behind the regional mortality difference in Finland. The findings highlight and give further support for the potentially important role of genetic risk factors in mortality….

“Our results correspond with known facts about mortality of middle-aged men in Finland. The death risk of Finnish speakers in western Finland is approximately ten per cent lower than that of Finnish speakers in eastern Finland, but 40% higher than that of Swedish speakers. These mortality differences resemble genetic mappings of the population, but no explicit link has yet been established….

“We find that mortality differences by people’s own birth area, which might proxy not only genetic factors but also early-life conditions, are fully explained by the parents’ birth area. If at least one parent was born in eastern Finland, the death risk is over 20% higher as compared with if both parents were born in western Finland.“

Relative death rates by region in Finland, standardised for age and calendar year, men aged 35-49 years, 1986-2005 . Total Finland is equal to one. The classification is according to the 20 administrative regions, plus one category (number 7) that separates the Helsinki metropolitan area.

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