Take white skin ;
http://en.wikipedia.org/wiki/White_people#Origins_of_light_skin
Skin color is a quantitative trait that varies continuously on a gradient from dark to light, as it is a polygenic trait, under the influence of several genes. Many of these genes have yet to be identified. However, two genes that are known to contribute to skin color are MC1R and SLC24A5.[35] The mutation resulting in the light skin version of the SLC24A5 gene has been estimated to have originated in Europe between 6,000 and 12,000 years ago, indicating that at least one of the genes responsible for pale skin colour in Europeans arose relatively recently.[41]
Mixed ancestry people of African-European descent who possess one or two copies of the European allele of the SLC24A5 gene have skin color that is significantly lighter than mixed ancestry people who possess only the African allele. It is estimated, based on this observation, that the SLC24A5 locus "explains between 25–38% of the European-African difference in skin melanin index".[38][42][43][44]
Therefore it appears that only a quarter of the whiteness of white skin relates to the SLC24A5 genes that evolved in the last 12,000 years.
That means 75 % of the whiteness can from other genes, as yet not analysed.
I suggest that 75 % of the genes for whiteness came from Neanderthal DNA and that positive sexual selection and natural selection created the SLC24A5 genes which evolved later on in Cro-Magnons.
Whiteness began with the Neanderthals as trait which had evolved in the Neaderthal population over the hundreds of thousands of years they had been living in Northern Europe, and when they bred with early Homo Sapiens that the genes for whiteness were inherited by the Cro-Magnons.
This led to the Cro-Magnons evolving more 'white genes' alongside the ones they had inherited from their Neanderthal ancestors.
It all fits.
White people are archetypically distinguished by light skin. Scientists discovered a skin-whitening mutation that largely explains the first appearance of white skin in humans between 20,000–50,000 years ago.
http://www.washingtonpost.com/wp-dyn/content/article/2005/12/15/AR2005121501728.html
In this paper it states " The work also reveals for the first time that Asians owe their relatively light skin to different mutations. That means that light skin arose independently at least twice in human evolution, in each case affecting populations with the facial and other traits that today are commonly regarded as the hallmarks of Caucasian and Asian races. "
This therefore tallies with the fact that the Neanderthal DNA suggests that there were two breedings with Homo Sapiens.
The gene did not arise 'independently' it means that there were two infusions of genes from Neanderthals that led to the white gene being inherited.
The first was with Asian Neanderthals who bred with Homo Sapiens around 50,000 years ago.
The second, I believe , was when another group of Homo Sapiens left Africa and bred with the Northern Neanderthals to become Cro-Magnons and this led to the birth of the White Race.
Those genes have since evolved to become the racial genes that pass on the racial features we see today.
Note the date when the white gene is estimated to have evolved in whites ;
" Although precise dating is impossible, several scientists speculated on the basis of its spread and variation that the mutation arose between 20,000 and 50,000 years ago. That would be consistent with research showing that a wave of ancestral humans migrated northward and eastward out of Africa about 50,000 years ago. "
This period when the white gene 'evolved' was when the Cro-Magnons evolved - and it was the period when the Neaderthals bred with Homo Sapiens after they left Africa.
The white gene did not evolve, it was passed to the Homo Sapiens who became Cro-Magnons around 40,000 years ago by breeding with the Northern Neanderthals.
This then fits us into the time window re blonde hair and blue eyes - and links us back to the Neanderthals again.
This is my theory.
The first group of Homo Sapiens left Africa around 50,000 years ago.
One group of Homo Sapiens met the Asian Neanderthal group in the North African region and bred with them - this led to the race group of the modern East Asians.
This is also why the Neaderthals in Asia disappeared around 50,000 years ago as they merged with the Homo Sapiens. These Asian Neanderthals had evolved to become a racial sub set of the Neanderthals living in that region and this is why the Homo Sapiens / Neanderthals who are Modern East Asians have different racial features to modern Cro-Magnon Whites.
Then around 40,000 years ago another group of Homo Sapiens moved out of Africa and into Northern Europe and met the Northern Neanderthal groups living in that region.
This group of Neanderthals were genetically different to the Neanderthals of Asia as they had evolved to become adjusted to the Northern European climate ( Neanderthals also had 'racial group's just as whites are genetically different to asians , Neanderthals also had racial differences ) and the Homo Sapiens in Northern Europe then bred with that group of Northern Neanderthals.
The Northern Neanderthals then vanished as they merged with the Homo Sapiens and became Cro-Magnons who evolved around 35,000 years ago.
This then explains ;
1) where the Neanderthals went - they became us
2) why both East Asians and whites have Neanderthal DNA but have different racial features as they derive from different Neanderthal groups - the East Asians inherited their yellow skin and racial features from the Asian Neanderthals.
The Neanderthals had themselves evolved into different Neanderthal racial sets over their 600,000 year evolutionary period of existence.
For example the Oase fossils which include a 40,000-year-old skull found in a Romanian cave that defies traditional anatomical categorization. Though the skull has the proportions of a modern human cranium, it has a retreating forehead and large upper molars among other features typical of Neandertals (SN: 3/24/07, p. 186). A similar jaw had previously been found at the site.
http://www.sciencenews.org/view/generic/id/58936/title/Neandertal_genome_yields_evidence_of_interbreeding_with_humans
http://en.wikipedia.org/wiki/Pe%C5%9Ftera_cu_Oase
The Oase Fossils, which seem to be at least three separate Human / Neaderthal groups or three different Neanderthal groups with different features proves that there were racial sub sets amongst the Neanderthal groups and different Neanderthal / Homo Sapien matings in history.
This is why modern East Asians have different features to modern Cro-Magnons, as the Neanderthal groups they evolved from were racially different Neanderthal groups.
3) where white skin, blonde hair and blue eyes came from which was the Northern Neanderthal group. These racial features were only in the Northern Neanderthal population.
4) that the SLC24A5 white genes arose in the Cro-Magnon group around 12,000 years ago. This is why whites have lighter skin than East Asians and why the SLC24A5 genes are only present in whites derived from Cro-Magnons.
Thats it.
This explains exactly where race and racial differences in modern Homo Sapiens comes from.