Archives for posts with tag: genes

look! a linkfest! (^_^)

Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia

37,000-year-old Russian skeleton has Neanderthal DNA that’s gone missing“Sequences present in its genome haven’t been found in modern human populations.” – see also Remix from greg cochran. – see also Genome of Kostenki-14, an Upper Paleolithic European (Seguin-Orlando, Korneliussen, Sikora, et al. 2014) from dienekes.

Humans Would Beat Neanderthals in Marathon

Different Ways to Color a Cat – from razib. – h/t billare! who tweeted: “Progenitors of modern Europeans were fairly light-skinned–why did a 2nd bout of selection leave its tell-tale marks?”

Admixture in the Americas: Introduction, partial correlations and IQ predictions based on ancestry – from emil kirkegaard.

Our Futile Efforts to Boost Children’s IQ“How can parenting and socioeconomic status play such minor roles in determining IQ, when scholars on all sides of the nature-nurture debate agree that somewhere around half of the variation in IQ is environmental? The short answer is that the environment that affects IQ doesn’t consist of the advantages that most people have in mind — parents who talk a lot to their toddlers, many books in in the house for the older children, high-quality schools and the like. Instead, studies over the past two decades have consistently found that an amorphous thing called the “nonshared” environment accounts for most (in many studies, nearly all) of the environmentally grounded variation. Scholars are still trying to figure out what features of the nonshared environment are important. Peers? Events in the womb? Accidents? We can be sure only of this: The nonshared environment does not lend itself to policy interventions intended to affect education, parenting, income or family structure.” – from charles murray. – h/t mr. mangan, esq!

Results of a “GWAS Plus:” General Cognitive Ability Is Substantially Heritable and Massively Polygenic – h/t emil kirkegaard!

Does neural crest development drive domestication syndrome?“Altered neural crest development could be the reason mammals change in oddly consistent ways during domestication. As first noted by Darwin more than 140 years ago, domestic mammals tend to share certain characteristics—a suite of traits called the domestication syndrome.”

‘Darwin’s Dilemma’ May Be Solved“Scientists following two different lines of evidence have just published research that may help resolve ‘Darwin’s dilemma,’ a mystery that plagued the father of evolution until his death more than a century ago. Biologists and geologists have been puzzled for decades over why life began so early on this planet, and then took so long to get interesting.”

A new study pieces together the puzzle of insect evolution“A new study of insect evolution — the largest of its kind ever undertaken — has uncovered some surprising new information, confirmed some long-held hypotheses and may lead researchers toward a more comprehensive understanding of evolution. One hundred scientists from 10 countries worked together to examine 144 insect species. Their goal was to create an insect ‘family tree’ and establish a timeline of insect evolution. Their results were published recently in the journal Science.” – cool!

More evidence that certain versions of some genes can encourage violence

Facial structure predicts goals, fouls among World Cup soccer players“The scientists studied the facial-width-to-height ratio (FHWR) of about 1,000 players from 32 countries who competed in the 2010 World Cup. The results, published in the journal Adaptive Human Behavior and Physiology, showed that midfielders, who play both offense and defense, and forwards, who lead the offense, with higher FWHRs were more likely to commit fouls. Forwards with higher FWHRs also were more likely to score goals or make assists.”

Mental health: Depression needs large human-genetics studies“To understand the molecular mechanisms of depression, collect genetic data from more than 100,000 people, says Steven Hyman.”

Geneticists tap human knockouts“On average, every person carries mutations that inactivate at least one copy of 200 or so genes and both copies of around 20 genes.”

The Inexorable Progress of Science: Archaeology“With a very limited set of clues, smart guys managed to get key facts about European prehistory roughly correct almost 90 years ago . With tremendously better tools, better methods, vastly more money, more data, etc, archaeologists (most of them) drifted farther and farther from the truth.” – from greg cochran.

How Your Facebook Updates Reveal Your Personality“Extroverts tend to use words like love, tonight, party, excited and amazing. Several length variants of the word soooo and ‘text speak’ terms like lovin and ur, are more often found on extroverts’ updates. In general the extrovert word cloud is sloppy enough to make any ‘Grammar Nazi’ red in the face. When we come to introverts, use of the word computer was one of the biggest giveaways. Posting status updates about Internet, and to a lesser extent anime, doctor who, and books, were also predictive of introversion.” – from neuroskeptic.

The contribution of additive genetic variation to personality variation: heritability of personality“[W]e found that approximately 52% of animal personality variation was attributable to additive genetic variation.”

The genetics of impulsivity: evidence for the heritability of delay discounting – h/t ben southwood! who tweeted: “Impulsivity is 55% heritable at age 18.”

We are not equally empathic – from peter frost.

He’s Definitely a Liberal—Just Check Out His Brain Scan“[W]e’ve had solid indications for a while now that our ideological biases are based, in large part, on the biology of our brains…. Of course, we’d like to think we came to our core beliefs through a process of rational reflection and discussion — or, at the very least, as a psychological reaction to the influence of our parents and peers…. But the profound influence of basic brain biology has just been re-affirmed in a new research paper, which found liberals and conservatives can be easily identified through fMRI scans…. ‘Remarkably,’ writes a team led by P. Read Montague of the Virginia Tech Carilion Research Institute, ‘brain responses to a single disgusting stimulus were sufficient to make accurate predictions about an individual subject’s political ideology.'”

The Most Heritable Gut Bacterium is… Wait, What is That?“By studying 416 pairs of British twins, Julia Goodrich and colleagues from Cornell University have identified the gut microbes whose presence is most strongly affected by our genes.”

Microbiome science threatened by contamination“Non-sterile sequencing returns rogue results in dilute microbe samples.”

Global IQ and health – from dr. james thompson.

Book Review: The Ten Thousand Year Explosion (2009) by Greg Cochran and Henry Harpending – from staffan.

The ecology of religious beliefs“Both comparative and experimental evidence indicate that beliefs in moralizing high gods promote cooperation among humans, a behavioral attribute known to correlate with environmental harshness in nonhuman animals. Here we combine fine-grained bioclimatic data with the latest statistical tools from ecology and the social sciences to evaluate the potential effects of environmental forces, language history, and culture on the global distribution of belief in moralizing high gods (n = 583 societies). After simultaneously accounting for potential nonindependence among societies because of shared ancestry and cultural diffusion, we find that these beliefs are more prevalent among societies that inhabit poorer environments and are more prone to ecological duress.”

Edvard Westermarck on Morality: The Light Before the Darkness Fell and Post-Darwinian, “Evolutional” Theories of Morality in the 19th Century – from helian.

Genes contribute to behavior differences between fierce and friendly rats“Genes active in the brain implicated in differences in rats selected for aggression or tameness”

Intimidating chimpanzee males are more likely to become fathers – ruh roh. – h/t steve stewart williams!

Marriage Records Reveal Patterns of Korean Migration Through the Centuries

What Edward Luttwak Doesn’t Know About Ancient China (Or a Short History of Han-Xiongnu Relations), pt. 1 and What Edward Luttwak Doesn’t Know About Ancient China (Or a Short History of Han-Xiongnu Relations), pt. 2 – from t.greer.

There’s Something About Teutonics – from those who can see.

An extremely low-density human population exterminated New Zealand moa“Here we show that the Polynesian population of New Zealand would not have exceeded 2,000 individuals before extinction of moa populations in the habitable areas of the eastern South Island. During a brief (<150 years) period and at population densities that never exceeded ~0.01 km(-2), Polynesians exterminated viable populations of moa by hunting and removal of habitat. High human population densities are not required in models of megafaunal extinction."

A Gene by Any Other Name“What is the logic in naming human genes?”

bonus: Keeping Mates Close and Competition Out in an Ocean Sponge

bonus bonus: Here’s Why Other People’s Farts Smell Way Worse Than Your Own – we cover *all* aspects of human biodiversity here on the hbd chick blog! (~_^)

(note: comments do not require an email. an ocean sponge.)

well this seems important! via race/history/evolution notes, an abstract from the society for molecular biology and evolution 2014 conference (in puerto rico! – teh scientists are always good to themselves whenever they can be (~_^) ):

Evidence for different mutation rates across human populations
Ron Do, David Reich
Department of Genetics, Harvard Medical School, Boston, USA

Although mutation rates (per base pair) have clearly changed across primate evolution, many analyses continue to assume that all present-day human populations have the same mutation rates. Recently, William Amos analyzed 1000 Genomes Project and Complete Genomics sequences and found evidence of significantly higher divergence rates on African than on non-African lineages since separation (W. Amos, PLoS One 4, e63048). The detected pattern was strongest in genomic regions of high polymorphism rate, a pattern that the author hypothesized was due to ‘heterozygote instability’, whereby gene conversion events surrounding heterozygous sites increase the mutation rate. To further test this observation, we measured the relative accumulation of mutations in lineages drawn from two different populations, using 25 deep genome sequences generated according to the same experimental protocol using the Illumina technology. We carried out pairwise comparisons of five sub-Saharan African (Dinka, Mandenka, Mbuti, San, Yoruba) and eight Non-African populations (Australian, Dai, French, Han, Karitiana, Mixe, Papuan, Sardinian) on all divergent sites. We observed statistically significant differences in the relative accumulation of mutations for many pairs of African and Non-African populations. Among the strongest differences is significantly more lineage-specific mutations in Mbuti than in Han Chinese (R=1.044, standard error (SE) =0.0015). On average, we observed about 1% more mutations on African lineages compared to Non-African lineages. We also observed some significant differences across non-African populations, with the Han Chinese who have experienced extreme expansions in population size associated with agriculture having more mutations than the Karitiana, a hunter-gatherer population from Amazonia who did not experience such expansions (R=1.015, SE=0.0014). The results are consistent across both European and African segments of the human reference sequence, so are not an artifact of reference sequence bias. Taken together, these results support the view that per-base pair mutation rates may be dynamically and substantially changing across humans.


wrt to greater number of mutations in african lineages: polygamy (and, therefore, older fathers)? life in the tropics?

(note: comments do not require an email. old san juan. (^_^) )

*update 10/27: for more on human leukocyte antigens (hla’s), see chris davies’ blog right here! (^_^)

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:]. 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:

– The Allele Frequency Net Database (AFND). A database and online repository for immune gene frequencies in worldwide populations: []
“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.” [].
– “AHPD: Analysis of HLA Population Data to Reconstruct the History of Modern Humans and Infer the Role of Natural Selection.” [].
“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.

**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

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


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