Archives for posts with tag: hla haplotypes

Ancient DNA Links Native Americans With Europe“…from the complete nuclear genome of a Siberian boy who died 24,000 years ago — the oldest complete genome of a modern human sequenced to date. His DNA shows close ties to those of today’s Native Americans. Yet he apparently descended not from East Asians, but from people who had lived in Europe or western Asia. The finding suggests that about a third of the ancestry of today’s Native Americans can be traced to ‘western Eurasia,’ with the other two-thirds coming from eastern Asia…. It also implies that traces of European ancestry previously detected in modern Native Americans do not come solely from mixing with European colonists, as most scientists had assumed, but have much deeper roots.” — see also: The First of the Mohicans from greg cochran.

Your face may have been sculpted by junk DNA“There is a huge degree of variation in human faces but, as family resemblances show, the overall shape is heavily constrained by genetics. However, so far, geneticists have identified only a small number of genes that influence the shape. These explain just a tiny fraction of the variation seen in human faces. According to Axel Visel of the Lawrence Berkeley National Laboratory in California and his colleagues, more variation is controlled by distant-acting enhancers. These are short sequences of DNA, in non-coding regions of the genome, that can influence the activity of the facial genes, even if they are a long way along the DNA strand.”

Behavior problems in preschool and child care centers may be an issue of genes“A new study suggests that some children may be genetically predisposed to developing behavioral problems in child care and preschool settings…. [B]irth parents who had high rates of negative emotion and self-control, based on a self-reported temperament scale, were more likely to have children who struggled with behavioral issues such as lack of self-control and anger, in child care centers. They controlled for adoptive parent’s characteristics, and still found a modest effect based on the genetic link.”

Your Ethnicity Determines the Species of Bacteria That Live in Your Mouth“[P]eople from each of the four different ethnic groups represented in the study (all participants self-identified as either Caucasian, African-American, Chinese or Latino) generally had similar species of bacteria, especially underneath the gums. As a result, simply by counting which varieties of bacteria appeared in this area, the researchers developed a model that was able to guess a person’s ethnicity with an accuracy significantly better than chance — it got it right 62 percent of the time. Some groups were even easier to identify via the bacteria than others: It could correctly identify Latinos 67 percent of the time and African-Americans with 100 accuracy. The variation along ethnic lines, they believe, is a reflection of genetics, not environment. That’s because, if you assumed that the mouth microbiome is totally dependent on environmental factors, you’d expect that members of the same ethnic group would have different mixes of bacteria depending on whether they were first-generation immigrants to the U.S. or had family histories that stretched back generations in the country. Instead, people’s background — in terms of foods they ate and other lifestyle trends — didn’t seem to have any correlation with the bacterial communities in their mouths. – h/t super bob!

Herpes virus genome traces the ancient path of human migration“Researchers…sequenced the genomes of 31 samples of herpes simplex virus type-1 to reconstruct how it hitchhiked on humans as they dispersed around the world. The results match the pattern proposed by the ‘Out of Africa’ theory, which has become the most widely accepted scenario for ancient human migration. The analysis showed that African strains of the virus contained the most genetic diversity — suggesting that they had the oldest roots.”

Genetic variation alters efficacy of antidepressant“Having a different form of a gene that regulates the brain chemical noradrenaline influences how well men remember negative memories after taking the antidepressant drug reboxetine, according to a study published in the October 23 issue of The Journal of Neuroscience. The findings demonstrate how genes can influence antidepressant response.” – see also: Genes predispose some people to focus on the negative.

Much Earlier Split for Neanderthals, Humans?“This suggests that the last common ancestor of H. sapiens and Neanderthals lived sometime earlier, perhaps as far back as one million years ago.”

Denisovans in Wallacea? – from greg cochran.

Life on Earth Was Not a Fluke“Figuring out how biomolecular self-organization happens may hold the key to understanding life on Earth formed and perhaps how it might form on other planets.” – h/t jayman!

Genetics made very simple – from dr. james thompson.

Low historical rates of cuckoldry in a Western European human population traced by Y-chromosome and genealogical data“[W]e estimate that over the last few centuries, EPP rates in Flanders (Belgium) were only around 1–2% per generation. This figure is substantially lower than the 8–30% per generation reported in some behavioural studies on historical EPP rates, but comparable with the rates reported by other genetic studies of contemporary Western European populations. These results suggest that human EPP rates have not changed substantially during the last 400 years in Flanders and imply that legal genealogies rarely differ from the biological ones.” – h/t rob brooks!

‘Endowment Effect’ Not Present in Hunter-Gather Societies“‘The more isolated Hadza traded about 50 percent of the time — which is what rational people should do,’ Azevedo said. People near the village traded about 25 percent of the time, which is much closer to the 10 percent we see with Western students.” – h/t jason collins! – previously: personality goes a long way… in which researchers find just big TWO personality traits in a group of hunter-gatherers (the tsimane).

speaking of the tsimane: UCSB anthropologist studies the evolutionary benefit of human personality traits“‘Being more extroverted, open, agreeable and conscientious –– and less neurotic –– was associated with having more kids.'” in tsimane men. (if they really have all those personality traits…see link immediately above.)

What Happens When a Language Has No Numbers? – on the pirahã. – h/t nn!

Can Your Genes Predict Whether You’ll Be a Conservative or a Liberal?“Scientific research shows political partisanship transcends economics, environment, and upbringing.” – from avi tuschman.

Life expectancy and the dawn of agriculture – from jason collins.

Origins of Americans (Looking At HLA Haplotypes) – from our very own chris davies! previously from chris: human leukocyte antigen (hla) haplotypes and human biodiversity.

Number sense in infancy predicts mathematical abilities in childhood“Preverbal number sense in 6-month-old infants predicted standardized math scores in the same children 3 years later. This discovery shows that number sense in infancy is a building block for later mathematical ability and invites educational interventions to improve number sense even before children learn to count.” – h/t simon baron-cohen!

Black Suits, Gowns, & Skin: SAT Scores by Income, Education, & Race – @the unsilenced science. see also: Obama Administration: Moynihan’s Law of Canadian Border kinda right from steve sailer.

Of Race and Intelligence – from helian.

Sex on the Mind“It is a truth universally acknowledged — at least by biologists — that every person owes his or her existence to parents who successfully reproduced, each of whom, in turn, had two parents who did the same … and so on, going back hundreds of millions of years to the first ancestral blob (or two) of protoplasmic goo that trundled onto terra firma from the early earth’s organic soup.” – from david barash. — see also: Why Have Sex? – from the advanced apes.

Lust Is Love – from heartiste.

Kids Are More Likely to Trust Attractive Adults – h/t hbd bibliography!

Asymmetries in altruistic behavior during violent intergroup conflict“Some empirical studies on intergroup conflict in hunter-gatherer societies and chimpanzees indicate that fitness relevant risks and potential benefits of attacks and defenses might have differed substantially under ancestral conditions. Drawing on these studies, it is hypothesized that the success of defenses was much more important for individual and kin survival and that a disposition to act altruistically during intergroup conflict is thus more likely to evolve for the strategic situation of defense…. Analyzing detailed historical case data from 20th century wars, this study finds that altruistic behavior towards members of the in-group indeed seems to occur more frequently when soldiers are defending themselves and their comrades against enemy attacks.” – h/t hbd bibliography!

Who gives? Multilevel effects of gender and ethnicity on workplace charitable giving.“[E]thnic minorities donate less money to workplace charity than do Whites.” – and men less than women. – via richard lynn @amren.

Paradoxes of the Nordic Model II“Denmark is a high trust, highly cooperative society. There is very low crime. Most parked bicycles are not even locked. Bank employees may not work very efficiently, but nobody tried to swindle me. In theoretical terms, what it means is that when there are very few defectors, the amount of common good produced overall is maximized. So everybody is well of, even though they don’t work hard – but they don’t free-ride, either….” – from peter turchin.

Ma’am, Your Burger Has Been Paid For – paying it forward in america! – h/t charles murray!

Napoleon Chagnon: The Fierce Sociobiologist“[Yanomamo] Men from the highland villages were much less belligerent than men from villages along the river. Heterogeneity in belligerence existed even within this single tribe.”

Where Have All the Geniuses Gone?

Aboriginal Hunting Practice Increases Animal Populations – monitor lizards, anyway.

“Science has lost its way, at a big cost to humanity“Researchers are rewarded for splashy findings, not for double-checking accuracy. So many scientists looking for cures to diseases have been building on ideas that aren’t even true.” – h/t outsideness! – see also: Trouble at the lab“Scientists like to think of science as self-correcting. To an alarming degree, it is not.”

These Unresolved Ethical Questions Are About to Get Real

bonus: Hunted by their own government – the fight to save Kalahari Bushmen“Survival International, which campaigns on behalf of tribal peoples, has called for tourists to boycott holidays in Botswana, which is forcing Kalahari Bushmen off their reserves.”

bonus bonus: How did ancient Greek music sound? – beautiful apparently! – h/t ed west!

bonus bonus bonus: Author: In China, ‘everyone is guilty of corruption’ – on guanxi.

bonus bonus bonus bonus: The couple having four babies by two surrogates“A British couple are to become parents of two sets of twin babies carried by two Indian surrogate women they have never met. Experts say twiblings – or children born to separate surrogates but created from the same batch of embryos – are not uncommon in India.”

bonus bonus bonus bonus bonus: Gang Rape in India, Routine and Invisible“[T]he Mumbai case provides an unusual glimpse into a group of bored young men who had committed the same crime often enough to develop a routine. The police say the men had committed at least five rapes in the same spot. Their casual confidence reinforces the notion that rape has been a largely invisible crime here, where convictions are infrequent and victims silently go away.” – see also: Trying to Make Sense of India’s Sexual Violence, State by State from t.greer.

bonus bonus bonus bonus bonus bonus: Insects aren’t gay, they’re just enthusiastic! Scientists discover same-sex mating in bugs is down to a rush to reproduce – h/t hbd bibliography!

bonus bonus bonus bonus bonus bonus bonus: Mysterious hum keeping people up all night ‘could be mating fish’“A council investigation was launched in Hythe, Southampton after some people had to move away because of the drone ‘pulsating’ through their homes.”

bonus bonus bonus bonus bonus bonus bonus bonus: Are conspiracy theories destroying democracy?“The more information we have about what governments and corporations are up to the less we seem to trust them. Will conspiracy theories eventually destroy democracy?” – h/t avi tuschman!

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

Advertisements

*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: 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!)