Archives for posts with tag: genes

Brown-skinned, blue-eyed, Y-haplogroup C-bearing European hunter-gatherer from Spain (Olalde et al. 2014) – @dienekes’. – also: European Hunter-Gatherers, Blue Eyes and Dark Skin? – from razib. – also: Hunter-gatherer European had blue eyes and dark skin“Genetic tests reveal that a hunter-gatherer who lived 7,000 years ago had the unusual combination of dark skin and hair and blue eyes.” – h/t ed west! – also: Tar-Zan* and Korak and Shades of Pale from greg cochran.

Y-chromosome “Adam” was not necessarily human“From the point of view of population genetics, there is absolutely no reason that the common ancestor of all human Y chromosomes must have existed in an individual that we would identify as ‘human’.”

Genomic variation in sharing between siblings“Visscher et al make really nice use of this slight variability in how much of the genome sibs share to learn about how much variation in height within a population is due to genetic variation. They use the fact that sibs who share slightly more of their genome (>0.5) should have more similar heights, than sibs who share less of their genomes (<0.5). This allows them to partition out how much of the resemblance between siblings is due to a shared environment, as opposed to shared genomes…. It also makes me wonder if sibs are actually unconsciously, weakly aware of these subtle genomic differences (through their similarity in a range of traits, including height etc). I could imagine doing a study where siblings (or others) are asked to assess how similar they are/feel, and then assessing whether this is weakly correlated with the fraction of the genome shared. I keep meaning to followup on this idea with some popgen theory to assess how this might play out in modifying kin-selection and altruism between sibs and other relatives." – from graham coop [this guy].

New genes spring, spread from non-coding DNA“A new study shows that new genes can spring from non-coding DNA more rapidly than expected.” – h/t hbd bibliography!

HBD Chick Lays it Down on HBD“I say can’t we just stick to seeking out the truth, whatever that is….” – hear, hear! – from jayman.

Diet rapidly and reproducibly alters the human gut microbiome“[T]he gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.”

300,000-year-old hearth found: Microscopic evidence shows repeated fire use in one spot over time“Scientists discovered in the Qesem Cave, an archaeological site near present-day Rosh Ha’ayin, the earliest evidence — dating to around 300,000 years ago — of unequivocal repeated fire building over a continuous period. These findings help answer the question and hint that those prehistoric humans already had a highly advanced social structure and intellectual capacity.” – h/t razib!

The new European phenotype: expansion into the Middle East – from peter frost.

Chimpocentrism and reconstructions of human evolution (a timely reminder) – h/t neuroskeptic! who said: “Beware ‘chimpocentrism’ in studies of human evolution.” – see also: Chimps have undergone more positive selection than humans – from adam benton.

Genius in the genes – from dr. james thompson.

On Dolphins, Big Brains, Shared Genes and Logical Leaps“‘It looks like ASPM evolved adaptively in all mammals…. It could be that ASPM is a general target of selection in episodes of brain evolution and isn’t specific to large brains.’”

Rates of atheism/agnosticism by ethnicity – from the awesome epigone.

Why Are Women More Liberal Than Men? – @the chateau.

Comparing Warfare Deaths per Capita in 18th vs. 20th Centuries“[T]he 20th century was only a bit more violent than the 18th century.” – from mike anissimov.

Why is polygamy declining? – from matt ridley, who tweeted: “The decline of human polygamy coincides with democracy.”

The Dark Enlightenment Hits Stage Two

La ciencia estúpida“La mayoría de los grandes científicos y filósofos no eran lo que diríamos tipos agradables. Tampoco eran políticamente correctos según el canon normal. Prácticamente ningún filósofo o científico anterior a la escuela de Frankfurt podría dar hoy una clase pública sin la amenaza de ser molestado por una turba emancipatoria. Hume, Darwin, Voltaire, Locke, Kant (no digamos ya Platón o Aristóteles) hoy no podrían ser contratados en la universidad de un país occidental.” – from eduardo zugasti.

Genome of longest-living cancer: 11,000-year-old living dog cancer reveals its origin, evolution“A cancer normally lives and dies with a person, however this is not the case with a sexually transmitted cancer in dogs. In a new study, researchers have described the genome and evolution of this cancer that has continued living within the dog population for the past 11,000 years.”

Why the masculine face? Genetic evidence reveals drawbacks of hyper-masculine features“[A]round half the variation in both male and female facial masculinity could be attributed to additive genetic variation…. The extensive genetic variation in masculinity makes more plausible the idea that choosing to mate with a masculine man can result in more attractive offspring. But the genes that made a male face more masculine did not make it more attractive. Worse, these same genes made female faces more masculine and thus less attractive. Families that make manly-looking sons tend also to make masculine-looking daughters.”

Casting Out The Devil“[C]onservatives generally think that liberals are misguided, and live in deep denial of obvious truths about human nature and the way the world actually works (as opposed to the way they think it *ought* to work), liberals view conservatives not just as misguided, but as *morally evil*.” – from malcolm pollack.

Joshua Greene’s “Moral Tribes”: The Minting of a New Morality – from helian.

Bones from human sacrifice at Tenochtitlan ceremonial complex“Fragments of human bones that exhibit cut marks and prolonged exposure to fire have been discovered through various excavations in the Sacred Precinct of Tenochtitlan (located in Mexico City). These skeletal remains are from individuals, such as children, slaves and captured warriors, who were sacrificed during religious festivals. – cannibalism! – h/t charles mann!

It’s not just ancient Roman propaganda: Carthaginians really did sacrifice children“‘We like to think that we’re quite close to the ancient world, that they were really just like us – the truth is, I’m afraid, that they really weren’t.’”

Data Mining Proves Darwin’s Finches Weren’t Really His – h/t jason moore!

Marry Your Like: Assortative Mating and Income Inequality“Does assortative mating contribute to household income inequality? Data from the United States Census Bureau suggests there has been a rise in assortative mating. Additionally, assortative mating affects household income inequality.” – h/t chuck ross!

Social status influences Democrats’ — but not Republicans’ — support for reducing inequality“Low wealth Democrats supported legislation to reduce economic inequality significantly more than both high wealth Democrats and Republicans. ‘Whereas Republicans tended to sponsor legislation that supports economic inequality regardless of their wealth, wealth predicted sponsoring behavior for Democrats,” the researchers explained.’ Specifically, high wealth Democrats tended to sponsor fewer pieces of legislation that reduce economic inequality than did their lower wealth counterparts.”

Dark lands: the grim truth behind the ‘Scandinavian miracle’“Take the Danes, for instance. True, they claim to be the happiest people in the world, but why no mention of the fact they are second only to Iceland when it comes to consuming anti-depressants?” – h/t claire lehmann!

Islam’s Baby Problem – @28 sherman.

Life as a Nonviolent Psychopath“Neuroscientist James Fallon discovered through his work that he has the brain of a psychopath, and subsequently learned a lot about the role of genes in personality and how his brain affects his life.” – this guy again. h/t ray sawhill!

A Sexual-Decision Flowchart That Makes Everything Simpler for Medieval Men – h/t jayman! (who’s prolly very glad he doesn’t live in the middle ages. (~_^) )

bonus: US Army considers replacing thousands of troops with robots“The US Army is studying whether robots could take the place of thousands of soldiers”

bonus bonus: Scotland had a glacier up to 1700s, say scientists

(note: comments do not require an email. glen coeglacial valley.)

*update 10/27: for more on human leukocyte antigens (hla’s), see chris davies’ blog right here! (^_^)
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over the past few months, commenter chris davies has left several interesting comments here on the blog about hla haplotypes (see here and here and here and here for example) — something about which, like so very many things, i know absolutely NOTHING.

i asked chris if he’d help alleviate my ignorance by writing a post on the topic, and he has graciously obliged (thanks, chris!). so, without further ado, here’s chris’ introduction to hla!:

An Introduction to HLA (Human Leukocyte Antigens)

I would like to thank HBD Chick, who recently asked me if I wanted to write a guest post here about Human Leukocyte Antigens (HLA). I have been a reader of this blog for several months now, and I really enjoy it. This blog is among the most innovative of the HBD-related blogs out there and takes a completely different approach to the subject. So it is a pleasure to write a post here, as I don’t write a blog myself.

In the comments section on some posts here recently I have talked about ‘HLA haplotypes’. I have had an interest in HLA haplotypes for a few years, following discussions with a molecular biologist who writes (or rather wrote) in newsgroups including Usenet. But what are ‘HLA haplotypes’, and more importantly what is their usefulness or relevance to those of us with an interest in ‘HBD’?

‘HLA’ means Human Leukocyte Antigen. The HLA system is simply the name given to the human version of the Major Histocompatibility Complex (MHC). MHC genes are found in most vertebrates, and this group of genes can be found on chromosome 6.

HLA genes are important in immune function and disease defence. There are three classes: Class I (A,B,C); Class II (DP, DM, DOA, DOB, DQ, DR); and Class III. All play different roles.

In addition to conferring resistance or susceptibility to various diseases and conditions (eg autoimmune diseases, such as type I diabetes), they are also vitally important in organ and bone marrow transplants. For example, if a donor is not a close enough match in terms of HLA, an organ could be rejected. Because diversity of HLAs in human populations is a part of disease resistance, it is very uncommon to find two unrelated individuals with identical HLA molecules at all loci.

In addition, it has been claimed that HLA may play a role in human mate selection through people’s perception of the odor of other people.

HLA haplotypes are like strings of HLA genes by chromosome, with one being inherited maternally and the other paternally. A multigene haplotype is a set of inherited alleles covering several genes, or gene-alleles. Common multigene haplotypes are generally the result of identity by descent from a common ancestor. As distance from the ancestor increases, chromosomal recombination causes multigene haplotypes to fragment.

An example of an HLA haplotype is shown below:

A*01:01 ; C*07:01 ; B*08:01 ; DRB1*03:01 ; DQA1*05:01 ; DQB1*02:01
[Which by serotyping, is more simply: A1-Cw7-B8-DR3-DQ2].

This particular haplotype btw is found at high frequency among people of North-West European descent, including Irish, British, Dutch, Germans, Scandinavians, and of course a high percentage of Americans and Australians. It is associated with autoimmune disorders like coeliac disease, and allergic diseases like hayfever and asthma.

In addition to medical use, HLA haplotypes can also be used as a means of tracing migrations in the human population as they are like a fingerprint of an event that has occurred in evolution.

So alongside Y Chromosome DNA and Mitochondrial DNA (mtDNA) markers, HLA haplotypes are useful tools for molecular anthropologists in determining evolutionary links between ancient and modern human populations. They also help to determine closeness of relationships between or within populations, and commonality of geographical origin between groups. Therefore patterns of migration and settlement can be traced, giving insight into how contemporary populations have formed and progressed over time.

Because the HLA system is under selection, diversity in HLA should be looked at in conjunction with other markers like Y-DNA and mtDNA in building a bigger picture when tracing migrations of modern humans.

However, HLA has several advantages over Y-DNA and mtDNA. mtDNA is often biased towards the founders in a core population and can show a punctuated distribution, while Y-DNA is biased more towards relatively recent migrations, and with both of these markers the effects of genetic drift are more rapid. With HLA there is intense heterozygous selection which works to preserve diversity.

Also with HLA, one tends not to see a punctuated distribution of haplotypes across geographical regions between groups, but rather one sees a fluidity of migrations tracing back to their original source population. Examples of this occur when one looks at diversity of HLA in northern Africa, which appears to be the source for a number of haplotypes that migrated into Europe in the Holocene. This picture is less clear from looking at mtDNA or Y-DNA data only.

Finally, the other advantage of HLA is the sheer volume of data available. [See: www.allelefrequencies.net]. The numbers of people worldwide who have been typed for HLA are huge. There are nearly 22 million donors and blood cord units in the BMDW (Bone Marrow Donors Worldwide) database, encompassing many different ethnicities and nationalities with hundreds of thousands of HLA alleles and extended haplotypes identified. Y-DNA and mtDNA cannot offer this volume of data. Whether used for tracing ancient human migrations, or researching diseases in different populations, this data can be extremely helpful.

The association of HLA haplotypes in populations with certain diseases in Western countries is interesting to consider from an HBD perspective. For example, if resistance or susceptibility to obesity, heart disease, diabetes, breast cancer, etc. are all affected by HLA type, then there could be wildly varying outcomes between different population groups, in addition to the effects of environmental or lifestyle factors.

This in turn could have serious implications. For example, certain disease-related charities’ fund-raising campaigns are aimed at convincing the general public to donate cash on the basis that everyone is almost equally at risk from that particular disease, when different ethnic groups living in the same country with the same lifestyle may often vary in risk considerably from very high risk down to very low risk, with HLA type being an important determining factor. But the charity may not publicise this information in order not to jeopardise their fund-raising. This, I should stress, is speculation on my part however.

If want to find out more about Human Leukocyte Antigens, please refer to some of the sources listed below:

References
- The Allele Frequency Net Database (AFND). A database and online repository for immune gene frequencies in worldwide populations: [www.allelefrequencies.net]
- “Tracking Human Migrations by the Analysis of the Distribution of HLA Alleles, Lineages and Haplotypes in Closed and Open Populations.” [Fernandez Vina, M. et al, 2012].
- “HLA 1991: Proceedings of the Eleventh International Histocompatibility Workshop and Conference” (Volumes I & II) [Kimoshi Tsuji; Miki Aizawa; Takehiko Sasazuki] Oxford Science Publications, 1991.
- “HLA-Net: A European Network of the HLA Diversity for Histocompatibility, Clinical Transplantation, Epidemiological and Population Genetics.” [www.hla-net.eu].
- “AHPD: Analysis of HLA Population Data to Reconstruct the History of Modern Humans and Infer the Role of Natural Selection.” [geneva.unige.ch/ahpd].
- “Challenging Views on the Peopling of East Asia: the Story According to HLA Markers.” [Di D, Sanchez-Mazas A.]. Am J Phys Anthropol. 2011 May; 145(1):81-96.doi:10.1002/ajpa.21470.Epub2011Jan4. PMID:21484761 [Pubmed – indexed for MEDLINE].
- Wikipedia: “Human Leukocyte Antigen.”
- Wikipedia: “Major Histocompatibility Complex.”

(note: comments do not require an email. gene map of the human leukocyte antigen (hla) region!)

Questions you never thought to ask: Is inbreeding bad for democracy? – i thought to ask. so did a few other people (way before me!): steve sailer, stanley kurtz, parapundit. see also Cousin Marriage and Democracy. and, of course, see also woodley and bell. and see Question of the Day @breviosity. previously: consanguinity and democracy.

A Dose of Clannishness and What’s So Bad About Clanocracy? – @breviosity!

Where do those tensions come from?“When the Milgram experiment was done with Jordanian assistants, they were just as willing as Americans to inflict pain under orders (62.5%). But they were more willing than Americans [1.4%] to inflict pain when no orders were given, with 12.5% of them delivering shocks right up to the top end of the scale (Shanab & Yahya, 1978).” – great post from peter frost!

Modern Europe’s Genetic History Starts in Stone Age“Scientists create the first detailed genetic history of modern Europe.” – original research article. see also mtDNA haplogroup H and the origin of Europeans (Brotherton et al. 2013) from dienekes.

As women live longer and have fewer children, they are becoming taller and slimmer, study finds“‘This is a reminder that declines in mortality rates do not necessarily mean that evolution stops, but that it changes.’”

Birth Defects, FBD Marriages – from anatoly.

HBD Fundamentals – from jayman!

Why the Tropics are an evolutionary hotbed“Ant family tree shows tropical New World hosts fast speciation while also keeping older lineages alive.”

Study: People Who Believe in God Are More Responsive to Treatment of Depression“It may be that ‘the tendency to have faith in conventional social constructs’ can be generalized both to religion and the medical establishment.”

Beauty isn’t skin deep – @mangan’s.

Social psychology fraud: Just tell professors what they want to hear – from steve sailer.

Book Review: Quiet – The Power of Introverts in a World That Can’t Stop Talking (2012) by Susan Cain – from staffan. and a classic: Caring for Your Introvert. (just shush already! (~_^) )

Ethnic origins of Forbes world billionaires (2013) – @race/history/evolution notes.

Computer scientists suggest new spin on origins of evolvability“‘[E]volvable species accumulate over time even without selective pressure.’” – in their computer simulations.

Culture — Not Just a Human Thing – vervet monkeys got culture. also Parrots Barter With Nuts.

Humans Evolved Flexible, Lopsided Brains – some of us more lopsided than others. (~_^)

When Do Babies Become Conscious?“New research shows that babies display glimmers of consciousness and memory as early as 5 months old.”

Fish win fights on strength of personality“When predicting the outcome of a fight, the big guy doesn’t always win suggests new research on fish.”

Feeding our gut bacteria meat may enhance heart disease risks“Antibiotics or vegetarian diets block production of a risk-associated chemical.”

On Hold: Genes That Pause Pregnancy Discovered

Giza Secret Revealed: How 10,000 Pyramid Builders Got Fed“This meat-rich diet, along with the availability of medical care (the skeletons of some workers show healed bones), would have been an additional lure for ancient Egyptians to work on the pyramids…. ‘They probably got a much better diet than they got in their village….’”

Earliest Mayan monuments unearthed in Guatemala. see also Ancient Maya discovery sheds new light on the origins of civilization.

bonus: Levels of Commitment to the Dark Enlightenment – @habitable worlds. also What are characteristics of the Dark Enlightenment? @occam’s razor.

bonus bonus: How Cuban Villagers Learned They Descended From Sierra Leone Slaves“The amazing story of the traditional songs and dances, passed down over hundreds of years, that have tied a small Caribbean ethnic group to a remote African tribe.” – cool story!

bonus bonus bonus: Revealed: The Indian village with just 6,000 inhabitants … but more than 100 pairs of twins – another town of twins!

bonus bonus bonus bonus: Can Animals Be Mentally Ill?

bonus bonus bonus bonus bonus: not a news story, but here’s the definition of stubborn – Last Two Speakers of Dying Language Refuse to Talk to Each Other

bonus bonus bonus bonus bonus bonus: Thanks to rare alpine bacteria, researchers identify one of alcohol’s key gateways to the brain“Discovery is a step on the road to eventually developing drugs that could disrupt the interaction between alcohol and the brain.” – cool! wait. they want to disrupt the effect of alcohol on the brain?! hey!

(note: comments do not require an email. vervet monkeys!)

lego dna

dna day. (^_^)

When the going gets tough, the tough get… more relief from a placebo?“[T]he new findings link specific, established personality traits with an individual’s susceptibility to the placebo effect…. The researchers showed a significant link between certain personality traits and how much relief people said they felt when given the placebo – as well as the level of a specific chemical that their brains released…. The findings show that about one-quarter of placebo response was explained by the personality traits of resiliency, straightforwardness, altruism or anger/hostility, as measured on standardized tests.”

Oxytocin Keeps Flirting Folks at Arm’s Length“[M]en who were in a committed relationship even maintained a greater distance from an attractive woman when under the influence of oxytocin than their control group.”

Gene distinguishes early birds from night owls and helps predict time of death“Common gene variant helps determine the time you will wake up each day — and the time of day you are likely to die.”

Link between creativity and mental illness confirmed“People in creative professions are treated more often for mental illness than the general population, there being a particularly salient connection between writing and schizophrenia.” – via parapundit.

Identical Twins Are Genetically Different, Research Suggests – copy errors.

The mysterious Ainu“[I]s the physical similarity [of the Ainu] to Europeans just a matter of chance? Convergent evolution? No, it may be that the Ainu have just not changed as much physically as other East Asians. – from peter frost.

Pre-Neolithic Mediterranean Island settlement“‘[T]he first inhabitants of many of the Mediterranean islands may not have been modern humans at all. Instead, he says evidence has been found that shows that they might have been Neanderthals, or Homo Erectus.’” – from dienekes.

Evidence for Early Hafted Hunting Technology“[E]arly humans were manufacturing hafted multicomponent tools ~200,000 years earlier than previously thought.”

The Golden Age“If people were always getting dumber, why on Earth would the scientific revolution be recent?” – greg cochran’s latest, most excellent rant. (^_^)

Einstein’s Brain“Uncommon features of Einstein’s brain might explain his remarkable cognitive abilities” – @the breviary (with appropriate and enjoyable sarcasm from mangan… (~_^) ).

Brain scans of rappers shed light on creativity“Functional magnetic resonance imaging shows what happens in the brain during improvisation.”

Why “Multicultural Society” is a Logical Impossibility

In Defense of Favoritism“Affective neuroscience research on early-childhood bonding suggests that, as mammals, we probably start out as emotionally glued microcommunities (family and tribe) before we become autonomous ego-driven creatures. Favoritism, not egoism, is probably the primal value system. In short, favoritism or bias toward your group is not intrinsically racist, sexist, or closed-minded. Privileging your tribe does not render you negative or bigoted toward those outside your tribe.”

bonus: Study Tracks Brain Gene Response to Territorial Aggression“Researchers are mapping the genetic underpinnings of the stickleback’s aggressive behavior.”

bonus bonus: Bonobos Catch Yawns from Friends

bonus bonus bonus: ‘Rogue planet’ spotted 100 light-years away“Astronomers have spotted a ‘rogue planet’ – wandering the cosmos without a star to orbit – 100 light-years away.”

(note: comments do not require an email. aggressive stickleback lurking in the foliage….)

**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.
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**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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here’s a really neat chart! (click on image for LARGER view. should open in new tab/window.):

what does it mean? well…

some very clever researchers/geneticists took a look for “runs of homozygosity” (roh) in the genomes of the individuals in the human genome diversity project (hgdp) — that’s 1043 individuals from 51 different populations. “runs of homozygosity” are stretches in the genome where identical dna was inherited from each parent. if you inbreed, you’re gonna have a greater number of longer runs of homozygosity in your genome than if you don’t.

apart from being just plain fun, sex shuffles up genomes from one generation to the next (presumably for some good reason or another). if you were to clone yourself, your descendants would have (pretty much) the same exact genome as you. if you were to mate with your mother or your sister (i know — ewwww!), your descendants would have different genomes from you, but they’d have lots of roh in their genomes ’cause their dna came from you and someone with whom you share a lot dna in common. the farther out you mate, the less homozygosity there’s likely to be.

you might also have lots of roh in your genome if you come from a population that has little genetic diversity — ’cause maybe your ancestors went through some sort of bottleneck or something.

inbreeding with close relatives — like marrying your first- or second-cousins (consanguineous matings) — leads to long roh since you share so much of your dna with your closest family members. endogamous mating — just mating within your population but not your close cousins — also leads to roh, but not ones as long as mating with your close relatives. you share dna with others in your population (say your clan or your ethnic group), but not so much of exactly the same dna or genes in certain stretches as with your closer relatives. a population will little genetic diversity, but that does not inbreed, will have lots of short roh — they share a lot of stretches of dna in common, but all of the outbreeding shuffles up the genomes within the population.

so that’s:

- long roh = inbreeding, probably consanguineous (first-/second-cousin matings)
- medium roh = endogmaous mating within a population
- short roh = little genetic diversity in the population probably from an event like a population bottleneck

i’m oversimplifying, but that’s the gist of it.

so what did the researchers find when they looked at the 51 populations in the hgdp (see chart)?

- LOTS of short roh (1-2 Mb) within populations from oceania and central/south america, probably because those populations went through bottlenecks. the people from oceania have low amounts of long roh (>16 Mb), which means that they don’t inbreed closely much. however, the people from central/south america have the highest amount of long roh of all the groups, so that’s means they must inbreed closely a LOT.

- central/south asians, west asians, east asians, europeans and africans don’t have huge amounts of short roh — at least not compared to the folks in oceania and the americas. no big bottlenecks there. and africans, in fact, have the fewest short roh.

- central/south asians and west asians have pretty high amounts of roh in all of the middle ranges and the highest long roh after the native american populations. this indicates significant amounts of endogamy and close relative marriages (but we already knew that).

- the groups with the lowest amounts of long roh are the europeans, africans and east asians — in that order. in other words, it appears as though, of these three groups, africans and europeans inbreed more closely (first- or second-cousin marriage, say) than east asians.

if you’ve been following along, you know that’s not what hbd chick expected. i thought that east asians would’ve had more short roh than europeans ’cause they have a fairly recent history of close marriages. hmmmm….

i checked to see which populations of europeans are included in the hdgp (you can find a list in the article’s supplemental material here [opens pdf]) and they are: adygeis, basques, french folks, italians, orcadians, russians, sardinians and tuscans. apart from the french and the tuscans, all of these groups have recent (or current) histories of consanguineous or endogamous mating practices (see Inbreeding in Europe series below in left-hand column for more details), so they are not a fully representative sample of europeans. unfortunately, “core” europe, which contains the most outbred populations in europe, is not included in the hgdp and, therefore, not in this study.

*sigh*

still — this is interesting stuff! genetics. cool! i’m going to post more about this ’cause, for one thing, it should be possible to drill down further into these populations to compare them more specifically (there are some data available in the supplemental materials). so, more anon…!

thanks to prof. harpending for pointing out this article! (^_^)

*update 08/20: see also runs of homozygosity again

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“Strangers can spot ‘kindness’ gene: study”

“People with a certain gene trait are known to be more kind and caring than people without it, and strangers can quickly tell the difference, according to US research published on Monday.

“The variation is linked to the body’s receptor gene of oxytocin, sometimes called the ‘love hormone’ because it often manifests during sex and promotes bonding, empathy and other social behaviors.

“Scientists at Oregon State University devised an experiment in which 23 couples, whose genotypes were known to researchers but not observers, were filmed.

“One member of the couple was asked to tell the other about a time of suffering in his or her life. Observers were asked to watch the listener for 20 seconds, with the sound turned off.

In most cases, the observers were able to tell which of the listeners had the ‘kindness gene’ and which ones did not, said the findings in the Proceedings of the National Academy of Sciences edition of November 14.

“‘Our findings suggest even slight genetic variation may have tangible impact on people’s behavior, and that these behavioral differences are quickly noticed by others,’ said lead author Aleksandr Kogan, a postdoctoral fellow at the University of Toronto….”

see also: Thin-slicing study of the oxytocin receptor (OXTR) gene and the evaluation and expression of the prosocial disposition @pnas.

p.s. – from the afp article:

“People in the study were tested beforehand and found to have GG, AG or AA genotypes for the rs53576 DNA sequence of the oxytocin receptor (OXTR) gene.

“People who have two copies of the G allele are generally judged as more empathetic, trusting and loving.

“Those with AG or AA genotypes tend to say they feel less positive overall, and feel less parental sensitivity. Previous research has shown they also may have a higher risk of autism.”

i got AG, btw. (~_^)

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