[Prosthetic Conscience]

Also related to this: DNA analysis of 7,000 year old remains from Spain indicate the man had dark skin (I can't tell if that means he didn't have the A111T variant), but blue eyes:

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.

It has surprised scientists, who thought that the early inhabitants of Europe were fair.

The research, led by the Institute of Evolutionary Biology in Barcelona, Spain, is published in the journal Nature.

The lead author, Dr Carles Lalueza-Fox, said: "One explanation is that the lighter skin colour evolved much later than was previously assumed."

Two hunter-gatherer skeletons were discovered in a cave in the mountains of north-west Spain in 2006.

The cool, dark conditions meant the remains (called La Brana 1 and 2) were remarkably well preserved. Scientists were able to extract DNA from a tooth of one of the ancient men and sequence his genome.

The team found that the early European was most closely genetically related to people in Sweden and Finland.

But while his eyes were blue, his genes reveal that his hair was black or brown and his skin was dark.

"This was a result that was unexpected," said Dr Lalueza-Fox.

Scientists had thought the first Europeans became fair soon after they left Africa and moved to the continent about 45,000 years ago.

"It has been assumed that it is something that happens in response to going from Africa to higher latitudes where the UV radiation is very low and you need to synthesise vitamin D in your skin. Your skin becomes lighter quite soon," explained Dr Lalueza-Fox.

"It is obvious that this is not the case, because this guy has been in Europe for 40,000 years and he still has dark skin."

http://www.bbc.co.uk/news/science-environment-25885519

Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe1, 2, 3. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet4. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

http://www.nature.com/nature/journal/va ... 12960.html

[Thunderhawk]

When they say dark skinned, do they mean tanned (common around the Med.), brown or darker?

[ThirdTerm]

Present-day European pigmentation traits are also derived from a late migration into Europe from South Siberia. During the middle Bronze Age, Andronovo nomads from Kurgans in South Siberia, who had fair skin, blue eyes and blond hair, infiltrated Europe in three waves between 4,400 and 2,800 BC. Around 4,400 BC, Kurgan people from the lower Dnieper and lower Volga regions began moving along the Black Sea littoral into the Danube Basin and they eventually colonised Germany and southern Scandinavia shortly after 3,000 BC. Andronovo nomads were the carriers of the R1a1 haplogroup and the Tarim mummies discovered in present-day Xinjiang also belonged to the same haplogroup. 77% of the ancient Kurgan mtDNA pool belonged to western Eurasian mtDNA haplogroups and the eastern Eurasian lineages were 23% of the sequences, indicating that the ancient Kurgan people were mixed-race people similar to the current inhabitants of Xinjiang Uyghur Autonomous Region and the Finno-Ugric peoples such as the Khanty and Mansi.


Gathering berries, Khanty people of Russia


Khanty girls

[foxdemon]

No, that's not what the authors think. This is a mutation that has proved beneficial in northern latitudes, to the extent of dominating western Eurasia and north Africa, and being fairly common in East Africa too. They think there was strong positive selection for it in Europe. It's not a 'loss of function' in northern latitudes, and wouldn't need an isolated population.

....

So they know it had spread widely through Europe before the Bronze Age, and it's most likely that the origin was west of Pakistan, not north.

Then the authors are mistaken. In fact the article you quoted shows their confusion.

Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations.

....

The geographical distribution of the A111T allele of SLC24A5 (Norton et al. 2007), updated with the use of additional population samples (Figure 1), shows that A111T is nearly fixed in all of Europe and most of the Middle East, extending east to some populations in present-day Pakistan and north India. A111T shows a latitudinal decline toward the Equator, with high frequencies in Northern Africa (>0.80), intermediate (0.4−0.6) in Ethiopia and Somalia, and lower (<0.35) in sub-Saharan Africa. This pattern is broadly consistent with strong positive selection for decreased skin pigmentation throughout Europe.

So they claim selection. But...

There is a cline of decreasing frequency of A111T in indigenous populations east of approximately longitude 75° in Central Asia, with near-absence in East Asia, Oceania, and the Americas. The extent to which the spread of A111T to the east has been inhibited by the absence of substantial eastward population migrations postdating its origin or by the presence of other loci responsible for decreased skin pigmentation in East Asia is presently unclear.

So they now use migration (and the implication of relatedness) in an attempt to explain away data that contridicts they selection hypothesis. It can also be argued that migration accounts for the western (or European) pattern of distribution of the allele in question. Infact the pattern happens to match what we know of the indo-euroepan migration history so migration is beyond doubt a better explaination to account for the pattern of distribution than is natural selection.




OK, so lets cut to the chase.


A common misconception of those who haven't studied evolutionary biology is that every phenotype must be of selective significance, that is to say, it is adaptive. This is not so. Richard Dawkin's famous example is the question: what is the adaptive advantage to the grasshopper by the kidneys being orange in colour?. The answer is that there is no advantage as there is not any adaptive significance to this phenotype. The material of the kidneys was going to reflect some wavelength of light and it happens to be orange. This will not in any way affect the survival of a grasshopper and thus won't impact the composition of the species' gene pool in the next generation.


So the problem here is that people who haven't studied evolution in detail, including otherwise very clever molecular biologists, think every feature of an organism needs an explaination of it's adaptive value. I say that the 'white pheonotype' has no adpative significance. It is only a result of stocastic genetics from small, isolatated populations which has been amplified by rapid growth of the population after fixation of the appropriate alleles.


The adpative hypothesis is falsified by the existence of peoples in very low sunlight environments without a fair phenotype. The Eskimos being a good example. If selection was so strong due to some overwhelming metabolic need (as is traditonally suggested to explain fair skinned phenotypes), we would expect all populations under such conditions to show the phenotype. This isn't so. Instead we see the phenotype limited to a particular allele and a particular ethnic group (though a wide spread one in the case of indo-europeans). This pattern fits a non adaptive, stocastic origin and historically contingent spread of the releveant genes.


By contrast, look at sickle cell amenia studies. We see clear evidence of balancing selection. Unrelated populations show similar selection for hetrozygotes for the sickle cell phenotype. This is selection at work. The argument for selection, and that implies some adaptive function for, the white phenotype simply doesn't exist.

[ThirdTerm]

With sufficiently strong positive selection for C11, it is possible that this haplotype could have originated anywhere within its current range and spread via local migration. However, selection acting in concert with major population migrations would have facilitated a much more rapid dispersal. Archeological, mitochondrial, and Y-chromosomal data suggest involvement of multiple dispersals in shaping the current populations of Europe and the Middle East (Soares et al. 2010). Because A111T is far from fixation in most Indian samples (Table S1), the high diversity of B-region haplotypes associated with C11 in the GIH sample may be the result of prolonged recombination rather than early arrival of A111T. In fact, the decrease in frequency of A111T to the east of Pakistan suggests that C11 originated farther to the west and after the initial genetic split between western and eastern Eurasians. On this basis, we hold the view that an origin of C11 in the Middle East, broadly defined, is most likely.

Afghanistan is geographically a part of the Greater Middle East located to the west of Pakistan and it's still the most likely place that the light-skin genetic mutation known as the A111T mutation occurred less than 50,000 years ago when Europeans genetically split from East Asians. The presence of a Caucasian population in Afghanistan also does not contradict the authors' observations about the possible geographical origin of A111T. East Asian haplotypes C3 and C10 are the precursors to C11 and the C11 people had to be isolated from East Asian populations for a certain period of time for such "prolonged recombination" to take place in a secluded environment that induced positive selection. The C11 or Kalash people subsequently spread to the western part of China and South Siberia, where western Eurasian haplogroups are found at high frequencies in local populations, before initiating their westward migrations.

Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

The La Braña individual discovered in Spain may have some African ancestry, which explains the lack of light skin pigmentation common in present-day Europeans. It's known that ancient African migrants extensively colonised Southern Europe, contributing up to 3% of the Southern European genome, and evidence of North African descent is highest in the Iberian Peninsula and the Canary Islands (up to 20%). The paper (Olalde et al. 2014) analysed the SLC45A2 and SLC24A5 pigmentation genes in the Mesolithic genome, the two strongest known loci affecting light skin pigmentation in Europeans, and found that the resulting haplotype comprises the SNPs that are absent in modern Europeans but present in Yorubans in southwestern Nigeria and southern Benin in West Africa. Analyses of additional ancient genomes from central and northern Europe will be needed to confirm how Europeans may have looked like 7,000 years ago.

[Prosthetic Conscience]

Afghanistan is geographically a part of the Greater Middle East located to the west of Pakistan

It's seem worth pointing out that your map shows Afghanistan to the north of Pakistan, not the west. It's still possible that A111T originated in Afghanistan, but it is less likely, because its spread into India has been limited, and it's unlikely that it would spread so well to the west, but not to the east.

You don't seem to have a reason to think Afghanistan is the most likely place; you're just asserting it. The authors on the paper, on the other hand, have set out their reasons for thinking it was further to the west.

[ThirdTerm]

A study (Rosenberg et al. 2006) showed that the Kalash people are a distinct or aboriginal population with only minor contributions from outside peoples and the Kalash formed one cluster in a cluster analysts (Figure 3). The cluster tree below shows that modern Europeans have descended from an ancestral group closely associated with the Kalash. Therefore, it can be reasonably concluded that the A111T mutation originally occurred in an ancestral group of the Kalash population and it was subsequently passed on to other Middle Eastern populations such as the Druze and Palestinians and then to various modern European populations located at the end of the blue-coloured Kalash branch of the cluster tree (e.g. Italian, French), which is consistent with the aforementioned migration patterns. Moreover, another genetic study (Firasat et al. 2007) analysed haplogroup frequencies among Kalash individuals and it found that there was a mixture of west and east Eurasian haplogroups. Haplogroup L (25%) and H (20.5%) have originated from prehistoric South Asia, while R1a (18.2%), R* (6.8%), R1* (6.8%), G (18.2%) and J2 (9.1%) can be commonly found in Europe and the Middle East, which shows that the Kalash people hold a special place in human evolution as the first group of people of Asian descent with the A111T mutation that gave rise to light skinned modern Europeans.

Figure 3. Consensus Neighbor-Joining Tree of Populations
The thickest edges have at least 95% bootstrap support, and the edges of intermediate thickness have at least 75% support. If all of the groups subtended by an edge have majority membership in the same cluster in Figure 2A (or only plurality membership in the cases of Hazara , Makrani, and Uygur), the edge is drawn in the same color as was used for the cluster.
doi:10.1371/journal.pgen.0020215.g003
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0020215

[Prosthetic Conscience]

The Kalash branch is coloured yellow, not blue.

The cluster tree below shows that modern Europeans have descended from an ancestry group closely associated with the Kalash.

It also shows that the Kalash have descended from an ancestry group closely associated with Europeans.

Therefore, it can be reasonably concluded that the A111T mutation originally occurred in the Kalash population

No, it can be reasonably concluded that it occurred in a population ancestral to both Europeans and the Kalash.

[R_G]

This could certainly be used as a tool to argue for the superiority of European Caucasians.

I'm sure one could chalk it up to evolution.


As for origins, the Middle East geographically was an advantageous area for growth. Not an indication of its advantages present day at all though.

[ThirdTerm]

A new study by the Oxford team (Hellenthal et al. 2014) further confirms the Kalash people's uniqueness in the history of human evolution and they have the oldest mixing in the dataset. Even though the methods used by the Oxford team have clear limitations and admixture events can only be detected for the last few thousand years, as the study failed to detect the Japanese people's dual Ainu/Yayoi ancestry, it estimates that the admixture event between an ancient European population and South Asian populations in the region occurred at some time between 990 and 210 BCE but it could possibly be much older. It also shows that the Kalash people are genetically similar to Scottish (4.8%), Irish (3.8%), Lithuanian (3.7%), German/Austrian (3.6%), English (3.3%) and Norwegian (3.2%), in line with the cluster tree above that shows that the Kalash, European and Arab populations had split from a common ancestry group that emerged in the region and modern Caucasian populations belong to the broadly defined Kalash cluster.

The group with the longest time since admixture is detected are the Kalash from Pakistan, with an ancient inferred event prior to 206 BCE, involving mixing between a more European and West Asian group, and a more Central/South Asian group (there may also be a contribution from people carrying DNA shared with modern-day East Asians, but we are less certain about this). Some Kalash believe they are descended from the army of Alexander the Great – our date does not rule this out but the date range also allows for many other possibilities. Other Pakistani groups also show equally ancient events with similar (but slightly less European-like) groups mixing. Other very ancient events involving completely different sources are also seen, for example in Ethiopians, and Russian people. All these populations have additional mixing events more recently. The geographical isolation of the Kalash might explain why they don’t show any recent event signal.
http://www.well.ox.ac.uk/~gav/admixture/2014-science-final/resources/FAQ.pdf