The term ‘Europoid’ has been used to refer to a population residing in Europe which can be defined as including any individual displaying homozygosity for the SLC45A2 rs28777-C allele, and the SLC24A5 rs1426654-G allele.
However, generic sequencing of early Anatomically Modern Homo sapiens (AMH) fails to reveal the derived SLC45A2 rs28777-C and SLC24A5 rs1426654-G alleles prior to 19,000-11,000YBP;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491390/#!po=47.1660
By studying compound haplotype systems within these genes, an attempt has been made to calculate the age of the alleles associated with lightening of European skin color. It is proposed that changes within KITLG appeared 30,000 years ago, and within TYRP1, SLC24A5 and SLC45A2 at 11,000-19,000 years ago, respective
The earliest homozygote for both SLC45A2 rs28777-C and SLC24A5 rs1426654-G is Motala man 8YBP;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750/
A second surprise is that, unlike closely related western hunter-gatherers, the Motala samples have predominantly derived pigmentation alleles at SLC45A2 and SLC24A5
This suggests that the Europoid population is only 8,000 years old, and indeed this model is nearly universally accepted in the literature. Claims of greater antiquity based on skull shape and other anatomical metrics are countered by the claim that the pigmentation of these ‘proto-Europoids’ was no lighter than any other population during the paleolithic.
However, genetic phenotyping allows us to explore novel allele combinations. Here, the authors attempt to substantiate the claim that some of these novel combinations resulted pigmentation as light as modern populations in the northern Mediterranean, such as Greeks, Italians and Spanish by modelling the resulting phenotypes via the HIrisPlex-S system; in addition, the authors observe that two of these these
combinations (Figures 6 and 7) result in p-values of 0.86-1 for Red hair, and all combinations result in a p-value of 0.338 for Blue eyes.
An unexplored path to Intermediate skin color (p-value = 1) and Red hair color (p-value = (0.86-1) exists in the MC1R gene, via a heterozygotic suite of rs1805005-T/ rs2228479-A/rs1805007-T/rs1805008-T alleles. The literature contains references to Red hair color induced both by homozygosity for a single MC1R allele as well as compound heterozygosity for multiple MC1R alleles;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1362956/
The desflurane requirement in redheads (6.2 volume-percent [95% CI, 5.9 – 6.5]) was significantly greater than in dark-haired women (5.2 volume-percent [4.9 – 5.5], P = 0.0004). Nine of 10 redheads were either homozygous or compound heterozygotes for mutations on the melanocortin-1 receptor gene
All of these alleles had emerged in an African population before the 70,000YBP Out-of-Africa date;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1288200/
On this time scale, ages for the Eurasian-distributed Val60Leu, Val92Met, and Arg163Gln variants are 250,000–100,000 years; the ages for African silent variants— Leu106Leu, Cys273Cys, and Phe300Phe—are 110,000–40,000 years. For the European red hair–associated Arg151Cys and Arg160Trp variants, we estimate an age of ꔆ80,000 years
rs1805005-T = Val60Leu, 250kya-100kya rs2228479-A = Val92Met, 250kya-100kya rs885479-T = Arg163Gln, 250kya-100kya rs1805007-T = Arg151Cys, 80kya rs1805008-T = Arg160Trp, 80kya
That only heterozygosity is required to display the phenotype depicted in Figure 6 is the principle argument; each allele could emerge on it’s own, and exist in a heterozygotic independently of the others. Since offspring would have a 25% chance of
inheriting heterozygosity for any one MC1R allele, as the alleles emerge in the population the likelihood of inheriting one of them increases with each allele added to the array.
Modeled via Punnett squares, assuming one AMH with 0/1 derived MC1R alleles and another with 0/0 derived MC1R alleles, the first genetation odds of inheriting the first allele – rs1805005-T – would be 50%. Adding the second, rs2228479-A allele, the odds of inheriting at least one allele becomes 75%. Adding the third, rs1805008 allele heterozygotically gives the Intermediate skin a p-value of 1, and it’s basic odds of being passed down is 87.5%.
Thus, the more derived alleles emerge, the higher the likelihood becomes that a derived allele will be passed down. In such a case, the model of a heterozygote breeding with another AMH who has no derived alleles must be replaced with a model including two heterozygotes. In such a case, two heterozygotes for 1 derived MC1R allele would have a 50% chance of producing a heterozygote, and a 25% chance of producing a homozygote. Two heterozygotes for 2 derived alleles would have only a 6.3% chance of producing a non-carrier for any derived MC1R alleles, and a 43.75% chance of producing a homozygote. Two heterozygotes for 3 derived MC1R allele would have a 53.125% chance of producing a homozygote for at least 1 MC1R allele, and only a 1.5625% chance of producing a non-carrier.
Two heterozygotes for all four derived MC1R alleles would have a 66.015625% chance of producing a homozygote of one of rs1805005-T, rs2228479-A, rs1805007-T or rs1805008-T, and only a 0.390625% chance of producing a non-carrier.
This entails that it would take 1.5 generations to produce two heterozygotes for any one allele from an initial heterozygotic mutant. In the next generation, two of the heterozygotic offspring could produce a homozygote for their MC1R alleles in 4 generations. Such a homozygote would highly bias inheritance towards the derived allele, producing many heterozygotes. Once two or more MC1R alleles were present in the population, the odds of inheriting at least one is so high as to assure their maintenence within the population.
The authors propose that once rs1805008-T had emerged and expressed heterozygotically, any individuals who possessed rs1805005-T and rs2228479-A would be born with Intermediate skin color, and sexual selection would enable this
rs1805008-T heterozygote to have many children who would bias their population towards their new skin color. rs1805007-T, causing Red hair within this genetic background, experienced the same sexual selection, leading to a population in Africa circa 80kYBP which displayed Red hair, Intermediate skin color and Blue eyes (p-value of 0.338.)
All four alleles are common in CEU, and rs1805005-T is displayed homozygotically by TSI (Tuscany, Italy) (Figure 8.) rs1805007-T (Figure 8) is displayed homozygotically by CEU. TSI is also homozygotic for rs2228479-A (Figure 9.)
Curiously, so is CHD (Chinese) (Figure 9.) CEU is not homozygotic for rs2228479-A, which absolutely precludes modern introgression. Instead, it suggests rs2228479-A is ancient in CHD, dating back to an introgression of Europoids after 70,000YBP.
Evidence for such an introgression can be traced via Y-haplogroup P1, which is native to the Philippines;
https://www.nature.com/articles/ejhg2014106.pdf
This pattern leads us to hypothesize a southeastern Asian origin for P-P295 and a later expansion of the ancestor of subhaplogroups R and Q into mainland Asia
Y-haplogroup P(P-295) emerged from Y-haplogroup-P1(P-M45,) and since Y-haplogroup-R is first found in Siberia;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105016
This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought
Acknowledging the low depth of coverage, we determined the most likely phylogenetic affiliation of the MA-1 Y chromosome to a basal lineage of haplogroup R
we have evidence of Philippines-to-Siberia gene flow which would have gone through
China – which explains the presence of rs2228479-A in CHD.
This implies that Europoids came from south of the Philippines. Y-haplogroup-P1 came from Y-haplogroup-P, which came from Y-haplogroup-K2b, which came from Y-haplogroup-K2. Today, basal Y-haplogroup-K2 is found exclusively among Australian aborigines. Y-haplogroup-K2 ultimately came from Y-haplogroup-F, which emerged in Melanesia;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1235276/
A Predominantly Indigenous Paternal Heritage for the Austronesian-Speaking Peoples of Insular Southeast Asia and Oceania
Like haplogroup C, haplogroup F therefore appears to have an origin in the south—in particular, in Melanesia
Y-haplogroup-F is, along with Y-haplogroup-C, one of the two founder Out-of-Africa Y-haplogroups which dates back to 70kya. These early colonists of Australia and Melanesia would have had Red hair and Intermediate skin color. This is proven by the presence of the rs2228479-A allele in Melanesia;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615358/
The most common MC1R mutations observed here are rs2228479 (V92M), rs885479 (R163G), and rs2228478 (T314T), which occur at frequencies of 15.4, 4.5, and 22.3 % in the resequenced sample, respectively.
We can also date the arrivial of Europoids by noting the earliest discovered example of Y-haplogroup-R – 14kya (Villabruna, Italy) in the case of Europe;
Note the high frequency of various derived MC1R alleles in Tuscany, Italy (Figures 8, 10). This could be a genetic trace left by Villabruna man. In contrast, CEU is the only population which displays homozygosity for the allele (rs1805007-T) that among the four, has the highest association for red hair (p-value 0.771 with heterozygotic rs1805005-T, rs1805007-T, rs1805008-T,) compared to rs2228479-A (p-value 0.148
with heterozygotic rs1805005-T, rs1805007-T.)
Interestingly, rs2228479-A with heterozygotic rs1805005-T, rs1805007-T, but without heterozygotic rs1805008-T, produces a p-value of 0.007 for Intermediate skin. Thus, rs1805008-T functioned in these archaic Europoids as a dominant trait to produce Intermediate skin color and Red hair.
Given the proposed Melanesian origin for Europoids (Y-haplogroup R,) the antiquity of their defining MC1R alleles (80kYBP) and the date of their arrival in Europe (14kYBP,) we can confidently state that Europoids emerged in Africa roughly 80kYBP, migrated to Sundaland and Sahul (here collectively referred to as Sundaland-Sahul,) and fled rising sea levels first to Indo-China, then India, and finally to the Caucacus and Europe starting around 14kYBP;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943878/
Additional evidence of an early link between west and east comes from the HERC2 locus, where a derived allele that is the primary driver of light eye color in Europeans appears nearly simultaneously in specimens from Italy and the Caucasus
~14,000-13,000 years agohttps://www.nature.com/articles/ejhg2014106.pdf
With the exception of P-P27, all of the descendant lineages are located today in Southeast Asia and Oceania: K-M526, K-P402, K-P261 and NO are the lineages most closely related to haplogroup K-P331, K-P397 is the sister lineage of P-P295 and the P-P295 lineages are the closest relatives of haplogroup P-P27 (Figure 1b). This pattern leads us to hypothesize a southeastern Asian origin for P-P295 and a later expansion of the ancestor of subhaplogroups R and Q into mainland Asia
However, given the geographic distribution of the P331 mutation, the immediate predecessor of P lineage and its likely origin in Southeast Asia/Indonesia, the existing evidence favors the first scenario. Interestingly, ancient DNA evidence suggests that haplogroup R1b – the current dominant lineage in western Europe – did not reach high frequencies until after the European Neolithic period
In sum, our results support the hypothesis of a Southeast Asian/ Oceanian center for the diversification of Oceanian K-haplogroup lineages and underscore the potential
importance of Southeast Asia as a source of genetic variation for Eurasian populations
Australian aborigines in fact display evidence of introgression from Indians;
https://www.pnas.org/content/110/5/1803
We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago
That this gene flow was into Indians from Australians is proven by the presence of Y-haplogroup-R in India;
https://www.frontiersin.org/articles/10.3389/fgene.2018.00004/full >Haplogroup R (38.5%)
This is one of the largest haplogroups in India and Pakistan. This is also the largest haplogroup
From somewhere in central Asia, some descendants of the man carrying the M207 mutation on the Y chromosome headed south to arrive in India about 10,000 years ago
Y-haplogroup-R emerged from a population movement out of the Philippines, and so the presence of R in Indians is evidence of India being the initial colony for Y-haplogroup R’s first carriers, who then proceeded northwest into Persia and the Caucacus, and from there to Siberia where MA-1 is found.
https://www.eva.mpg.de/documents/Elsevier/Yang_40000-year-old_CurrBiol_2017_2488539.pdf
Lipson and Reich [19] find that the 24,000-year-old Malʼta1 [20] and 16,500-year-old AfontovaGora3 [4] from western Siberia and several 7,000- to 14,000-year-old Western Eurasian individuals show evidence of gene flow from a population related to the East and Southeast Asian Ami
Prior to this, roughly 37kya, Europoids colonized Africa and bred with local hominids. They brought African-Melanesian hybrids back to Sundaland-Sahul, and this is how the
derived, African MSFD12 allele introgressed into Melanesians;
https://penntoday.upenn.edu/news/penn-led-study-identifies-genes-responsible-diversity-human-skin-colors
Another region, which contains the MFSD12 gene
The team found that mutations in and around this gene that were associated with dark pigmentation were present at high frequencies in populations of Nilo-Saharan ancestry, who tend to have very dark skin, as well as across sub-Saharan populations, except the San, who tend to have lighter skin. They also identified these variants, as well as others associated with dark skin pigmentation, in South Asian Indian and Australo-Melanesian populations, who tend to have the darkest skin coloration outside of Africa
Some have argued itʼs because of convergent evolution, that they independently evolved these mutations, but our study finds that, at genes associated with skin color, they have the identical variants associated with dark skin as Africans
Our data are consistent with a proposed early migration event of modern humans out of Africa along the southern coast of Asia and into Australo-Melanesia and a secondary migration event into other regions