December 03, 2011

Selection for skin color: not so simple

Investigative Genetics 2011, 2:24 doi:10.1186/2041-2223-2-24

Contrasting signals of positive selection in genes involved in human skin color variation from tests based on SNP scans and resequencing

Johanna Maria de Gruijter et al.

Abstract (provisional)
Background
Numerous genome-wide scans conducted by genotyping previously-ascertained single nucleotide polymorphisms (SNPs) have provided candidate signatures of positive selection in various regions of the human genome, including in genes involved in pigmentation traits. However, it is unclear how well the signatures discovered by such haplotype-based test statistics can be reproduced in tests based on full resequence data. Four genes, OCA2, TYRP1, DCT and KITLG, implicated in human skin color variation, have shown evidence for positive selection in Europeans and East Asians in previous SNP-scan data. In the current study, we resequenced 4.7-6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians and South Asians.

Results
Applying all commonly-used allele frequency distribution neutrality test statistics to the newly generated sequence data provided conflicting results in respect of evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. The application of Markov Chain Monte Carlo Approximate Bayesian Computation to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection as previously detected with sequence-based and some haplotype-based tests.

Conclusions
Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.

Link

17 comments:

apostateimpressions said...

It seems intuitive that European geography, climate and society would have selected for European genetic traits over thousands of years. I dont know how comfortable scientists are with that idea these days, as it implies that i) Europe is the adaptive home of Europeans, ii) non-European are not adapted to Europe, iii) selective pressures will continue to apply to non-Europeans within Europe so as to eventually select traits already present in Europeans. Europeans became Europeans for precise scientific reasons. Those implications seem uncomfortable for the current egalitarian political agenda of mass immigration into Europe. It raises the question of whether anthropology has anything to teach politicians -- and whether anthropologists will surrender theoretical integrity under social pressure.

Dienekes said...

There's no such thing as "European geography, climate and society". Different parts of Europe have had (historically) more similarities in all these factors to parts of Asia and Africa rather than to other parts of Europe.

apostateimpressions said...

D, thats a fair point and I should have been more precise. Im looking from my perspective here in England. Obviously we are on a cold island in the far north with little direct sunlight during the winter months due to cloud cover. It seems to me that South Asians and SS Africans are ill adapted to this climate and that in the long run natural selection will favour indigenous genes over those better suited to much hotter climes. Moreover, it is obviously desirable that people should be well adapted to their environment.

Mass immigration has been made possible very recently by advanced industrial capitalism. But -- given peak oil and oil crunches -- how many would survive a single winter on this island without oil and gas to keep them snug? Tens of thousands of pensioners freeze to death here every winter because they cannot afford fuel bills. Household energy bills will be 40% higher this winter than last winter, which was remarkably pricey. Crude oil is bobbing around the $110 a barrel mark, 50% up from 2007 and leading official commentators in the UK media (heads of banks and bodies) are beginning to suggest that high energy prices are the real reason why economies cant grow and repay debts. If capitalism collapses because profit margins have been eradicated, then likely the population will also collapse. So natual selection may kick back in big time in our lifetimes and even really soon.

Capitalism works through short term economic needs but political philosophy should look to the deeper, long-term causes of things and plan further ahead. I feel that anthropology, taken seriously, has a lot to teach us about how human societies function and I see clear basic tendencies of humans to form distinct ethnic groups and to adapt to particular areas. Late capitalist "globalism" presents opposite tendencies and I suspect that it will soon lead to chaos and disaster.

Derek said...

Is there any hint in the paper of when the selection may have occurred?

Dienekes said...

D, thats a fair point and I should have been more precise. Im looking from my perspective here in England. Obviously we are on a cold island in the far north with little direct sunlight during the winter months due to cloud cover. It seems to me that South Asians and SS Africans are ill adapted to this climate and that in the long run natural selection will favour indigenous genes over those better suited to much hotter climes. Moreover, it is obviously desirable that people should be well adapted to their environment.

Humans, unlike other animals, adapt to their environment by a combination of cultural and biological means. Warm-blooded animals that venture to the north had better have furs, thick skin, and a great system for converting calories into heat, otherwise they'll die. Humans, on the other hand didn't grow fur when they moved to cold latitudes, they used warm clothing, fires, and the intelligence to hunt and move about when it's possible and retire in shelter when it's not.

Similarly, Englishmen who went to Australia and Germans who went to Mexico are not doomed by the fact that they're ancestors evolved in different environments, because they can use culture to survive and even thrive.

Certainly, modern technological civilization with its air conditioning, electric lights, fossil fuels, etc. makes it possible for people to live outside their comfort zone without any significant problems. But, it's rather pessimistic to plan for a future when all these comforts will be taken away, and, certainly if civilization is wiped out by some major catastrophe, mankind will most likely find a new balance, as it did when much greater geological and climatic upheavals took place in the history of the Earth.

Onur said...

I agree with Dienekes' points. Human adaptation to environment includes both cultural and biological means (in varying combinations). Human racial differences is another issue. There is no magical line that separates the continents of Europe and Asia; Europoid, Caucasoid and White are all terms that are identical in meaning and include, in addition to Europeans, all of West Asians (except some significantly Negroid-admixed south Arabians), most of North Africans and a minority of North/Central/South Asians (mostly those living in parts adjacent to Europe/West Asia).*

* I am categorizing current people's locations according to the pre-1492 locations of their ancestors.

Amanda S said...

Also there's really no evidence that light-skinned Europeans feel the cold any less than other groups.

The only cold climate adaptation I've ever heard of is amongst Australian Aborigines who, according to a doctor friend of mine, have an ability to keep the blood vessels on the front part of their bodies open whilst the ones at the back of the body restrict. This would be a cold weather and camp fire adaptation. I'm sorry but I can't find any online references to confirm or refute this.

It's true that there were some cases of rickets appearing amongst South Asians when they first moved to the UK due to cultural practices of covering large parts of the body and staying out of the sun but I doubt these would happen today. It's not that hard for people to get sufficient vitamin D with modern diets and some sun exposure in northern climes not to reduce their ability to reproduce.

Amanda S said...

Sorry for the back to back posting but I've found an article about cold adaptation in Aborigines which is perhaps a little different than I suggested above. Here is the link.

http://jap.physiology.org/content/13/2/211.short

Jim said...

"Humans, unlike other animals, adapt to their environment by a combination of cultural and biological means. "

To the extent we can. It was only recently that we humans identified vitamin d deficiency as the probnlem it is and found ways to dela with it. Her in the Psacific Northwest it is a problem even among whites and may be linked to the higher than normal incidence of multiple sclerosis here. It has also been linked to immune system problems and may contribute todiabetes and asthma, which African Americans suffer from more than the rest of the population. Of course there are measures we can take, but it can take centuries.

Yes whites adapted to Australia, but after all a lot of Australia has a Mediterranean climate. But that wasn't true of all the colonies. David Hackett Fischer (Albion's Seed) showed from death records that in the 1600s the African death rate in Massachussetts was double that of europeans, equal in the mid-Atlantic colonies and reversed in Virgina. And the Carolinas were nortorious as death for Englishmen. Over the centuries people did adapt, but it was not as simple as building better houses or chopping more firewood.

Roy said...

“..they appear as a distinct, unmixed race, like none but themselves. Hence, too, the same physical peculiarities throughout so vast a population. All have fierce blue eyes, red hair, huge frames, fit only for a sudden exertion. They are less able to bear laborious work. Heat and thirst they cannot in the least endure; to cold and hunger their climate and their soil inure them“

Jim said...

"“..they appear as a distinct, unmixed race, like none but themselves. Hence, too, the same physical peculiarities throughout so vast a population. All have fierce blue eyes, red hair, huge frames, fit only for a sudden exertion. "

Indeed. It describes no extant German-speaking population, does it?

pconroy said...

Amanda S said:
Also there's really no evidence that light-skinned Europeans feel the cold any less than other groups.

Not true!

I go outside wearing a T-shirt at 50 F or above, and wear a light jacket or sweater at 40-50 F, and only wear a heavier jacket below 35 F or near freezing.

In contrast, I notice African-Americans on the subway here in New York, will be wearing parkas and down-quilted long coats at 40 F, at about 35 F they will be wearing multiple hoodies, parkas, thick scarves and padded gloves.

I never owned a hat or gloves in Ireland, and only wear them when the temperature is below 30 F.

As Roy notes, I however can't stand humidity or heat at all, and am lethargic at above 70% humidity or 80 F, and can't tan, so need to wear long sleeved shirts in summer.

So your equalism is BS!

Jim said...

"Amanda S said:
Also there's really no evidence that light-skinned Europeans feel the cold any less than other groups.
Not true!"

In the US Army an important paert of trianing first-line leaders in watching for cold and heat injuries in their people is to get the white leaders to remember that their black soldiers may be developing frostbite before the white leader feels the cold suficiently to start worrying about it. But that is only frostbite; I don't recall anything similar for hypothermia, where body fat ratios are likelier to be what makes the difference.

It is different with heat - no one has any particular innate adaptation. What matters with ehat is acclimation. The rule of thiumb on that is to allow a full month in country before expecting soldiers from colder climates perfomer at the same level of physical exertion as back wherever they deployed from.

pconroy said...

@Jim,

I've been in New York over 20 years and have never adapted to the heat, I can't.

I'm a huge sweater, and in summer when it's hot and humid, and I'm outside, I've fainted a number of times - mostly due to dehydration, caused by copious sweating.

Our nanny - an Afro-Caribbean from Trinidad - meanwhile is always turning up the heat in the house, and thinks we keep the place too cold. When I get home in the evenings, the first order of business is to open the windows and let some excess heat out!

Amanda S said...

Jim, thanks for the information from the Army.

pconroy, I love the way that you generalise from your own experience. For myself I don't miss chilblains and the permanently bluish hands I used to have through the English winter.

It occurs to me that one other environment which biological adaptation outstrips technological adaptation is high altitude environments. I'm thinking of Tibet and the Andean Altiplano. I know that individuals do adapt somewhat to these environments but that it is nothing compared to those whose ancestors have lived in them for many generations. I would think that in living a more active life the adapted individuals could well have a reproductive advantage against lowland incomers.

Jim said...

"I'm a huge sweater, and in summer when it's hot and humid, and I'm outside, I've fainted a number of times - mostly due to dehydration, caused by copious sweating."

Pat, you are aware you sweat copiously because you are in a humid climate. Humidity reduces the effectiveness of sweating - no humans are really adapted to humid climates. You mention dehydration - how much water or do you drink when it gets hot? You've been in NY for 20 years, but if you retain your drinking habits from Europe, the dehydration is not surprising.

Something else, and this is folklore, so get the salt - but a meat-heavy diet is supposed to go with heavy seating.

"I know that individuals do adapt somewhat to these environments but that it is nothing compared to those whose ancestors have lived in them for many generations. "

But even then, they may not really be living in the same environment as the local people - better clothing, better shelter...

apostateimpressions said...

It is true that immigrants from hot climes may be able to "adapt" culturally but that doesnt change the fact that they are not biologically adapted to northern parts like Britain and Ireland. Northern Europeans ALL took on fair skin because it provided evolutionary benefits over ALL those without the adaptation. Northern Europeans have adapted to the north over thousands of years of relentless natural selection. It is obviously desirable that people should be well-adapted to their environment and it is equally obvious that mass immigration from black countries will leave the breed less well-adapted. It is radically naive to pretend that doesnt matter because of some imaginary "moral" agenda. Somehow it is imagined that society has the "right" to by-pass basic anthropological common sense because it is supposedly "good" and "nice" when we do that. That mentality is totally contrary to Nature, which works through the survival of the fittest and the constant elimination of the ill-adapted. Are we going to say that Darwin was wrong or just ignore everything that he taught us? This is 2011 and we might as well be back in the Middle Ages. We have as a civilization learnt absolutely nothing. The only "truths" that we can hold up are "moral" garbage about "inalienable rights".