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The fact has been brought up countless times in this forum that Africans possess the greatest genetic diversity, yet oddly among some individuals skin color variation especially light skin in Africans is attributed to foreign (Euasian) admixture but how true is this, especially in regards to the Khoisan aboriginals of Southern Africa??
To begin with is a primer on the genetics of skin color variation in Africans as based particularly on the 2017 study by Sarah Tishkoff et al.:
The Varying Skin Colors of Africa: Light, Dark, and All in Between “When people think of skin color in Africa, most would think of darker skin,” Tishkoff says, “but we show that within Africa there is a huge amount of variation, ranging from skin as light as some Asians to the darkest skin on a global level and everything in between.”
Some of the genetic variants the researchers identified, coding for both light and dark skin pigmentation, were quite ancient, between 300,000 and 1 million years old, meaning that skin color variation seems to have been present since before the emergence of Homo sapiens.
Tishkoff noted that the work underscores the diversity of African populations and the lack of support for biological notions of race.
“Many of the genes and new genetic variants we identified to be associated with skin color may never have been found outside of Africa because they are not as highly variable,” Tishkoff says. “There is so much diversity in Africa that’s not often appreciated. There’s no such thing as an African race. We show that skin color is extremely variable on the African continent, and that it is still evolving.”
New Gene Variants Reveal the Evolution of Human Skin Color The study, published online this week in Science, traces the evolution of these genes and how they traveled around the world. While the dark skin of some Pacific Islanders can be traced to Africa, gene variants from Eurasia also seem to have made their way back to Africa. And surprisingly, some of the mutations responsible for lighter skin in Europeans turn out to have an ancient African origin.
The team also found variants of two neighboring genes, HERC2 and OCA2, which are associated with light skin, eyes, and hair in Europeans but arose in Africa; these variants are ancient and common in the light-skinned San people. The team proposes that the variants arose in Africa as early as 1 million years ago and spread later to Europeans and Asians. “Many of the gene variants that cause light skin in Europe have origins in Africa,” Tishkoff says.
The most dramatic discovery concerned a gene known as MFSD12. Two mutations that decrease expression of this gene were found in high frequencies in people with the darkest skin. These variants arose about a half-million years ago, suggesting that human ancestors before that time may have had moderately dark skin, rather than the deep black hue created today by these mutations.
These same two variants are found in Melanesians, Australian Aborigines, and some Indians. These people may have inherited the variants from ancient migrants from Africa who followed a “southern route” out of East Africa, along the southern coast of India to Melanesia and Australia, Tishkoff says. That idea, however, counters three genetic studies that concluded last year that Australians, Melanesians, and Eurasians all descend from a single migration out of Africa. Alternatively, this great migration may have included people carrying variants for both light and dark skin, but the dark variants later were lost in Eurasians.
two natives of Ethiopia
And now here's a 2018 study from Brenna Henn et al.:
An Unexpectedly Complex Architecture for Skin Pigmentation in Africans Summary Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan, populations indigenous to southern Africa, who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13 using a genome-wide association approach complemented by targeted resequencing. By considering diverse, understudied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.
Introduction Skin pigmentation is one of the most strikingly variable and strongly selected phenotypes among human populations, with darker skin observed closer to the equator and lighter pigmentation observed at high latitudes (Sturm and Duffy, 2012). Researchers have hypothesized that variable exposure to ultra violet radiation (UVR) creates opposing selective forces for vitamin D production and folate protection, resulting in variable melanin production and global pigmentation differentiation (Chaplin and Jablonski, 2009; Jablonski and Chaplin, 2010). Skin pigmentation differences at similar latitudes and UV exposures indicate that additional evolutionary forces, such as assortative mating, drift, and epistasis, are also likely to have affected global skin pigmentation (Pospiech et al., 2014; Wilde et al., 2014). While ~171 genes have been implicated in variability across model organisms (e.g. the Color Genes database: http://www.espcr.org/micemut/), only ~15 genes have been associated with skin color differences in humans (Table 2). The relative paucity of loci identified from GWAS efforts has led to the characterization of pigmentation variation as relatively simple, with only a handful of SNPs being highly predictive of skin, eye, and hair color across populations (Hart et al., 2013a; Spichenok et al., 2011; Walsh et al., 2013)... Despite being home to the greatest range of pigmentation globally, remarkably few genetic studies of pigmentation have been published to date in continental Africans (Jablonski and Chaplin, 2014; Relethford, 2000). Instead, the genetic basis of skin color has primarily been studied in Eurasians and admixed African Americans (Beleza et al., 2013; 2012; Candille et al., 2012; Sturm and Duffy, 2012; Sulem et al., 2008; 2007); selective sweeps in high latitude populations have been interpreted as resulting from strong environmental selection pressure. For example, the derived Ala111Thr allele (rs1426654) of SLC24A5 that swept to near fixation in western Eurasian populations confers the largest known effect on skin color variability (Beleza et al., 2013; Lamason, 2005). Loci in/near SLC45A2, GRM5/TYR, and APBA2/OCA2 also have divergent allele frequencies between Europeans and Africans, with large derived lightening effects in Europeans (Beleza et al., 2013; Norton et al., 2006). Smaller effects contribute to the relatively narrow variation within Europeans, including associations in/near MC1R, TYR, IRF4, and ASIP (Sulem et al., 2007; 2008). Several shared lightening effects derived in Eurasians arose through convergent evolution (e.g. rs1800414 in OCA2 in East Asians), whereas other shared effects resulted from similar selective sweeps (e.g. KITLG) (Miller et al., 2007; Yang et al., 2016). Because African populations have been understudied, the genetic architecture and higher variability of skin pigmentation is poorly understood…
Striking skin pigmentation variability among African populations has been underappreciated in genetic studies (Jablonski and Chaplin, 2014; Relethford, 2000). Light skin pigmentation is observed in the far southern latitudes of Africa among KhoeSan§ hunter-gatherers and pastoralists in and near the Kalahari Desert. The KhoeSan are unique in their early divergence from other populations, likely dating back at least ~100,000 years ago (Schlebusch et al., 2012; Veeramah et al., 2011); they exhibit extraordinary levels of genetic diversity and low levels of linkage disequilibrium (LD) (Henn et al., 2011). Previous work points to southern Africa as the point of origin for modern humans (Henn et al., 2011; Tishkoff et al., 2009), but it is unknown whether moderate to light skin pigmentation in the different KhoeSan groups is an example of convergent evolution with northern Europeans and Asians, or reflects the ancestral human phenotype. Previous studies have noted different pigmentation allele frequencies between the Ju|’hoansi San and other Africans, but these have been based on n<7 individuals from the former population without measured phenotypes (Berg and Coop, 2014; Norton et al., 2006).
Here we report an evolutionary and genetic study of skin pigmentation with a total of 465 genotyped KhoeSan individuals (278 ‡Khomani San and 187 Nama), with targeted resequencing at associated pigmentation loci and matched quantitative spectrophotometric phenotype data (Table S4). The ‡Khomani San are traditionally a N|u-speaking hunter-gatherer population living in the southern Kalahari Desert, while the Nama are traditionally a Khoekhoe-speaking semi-nomadic pastoralist group of KhoeSan ancestry. We investigate: i) the degree of polygenicity and heritability of skin pigmentation, ii) the extent of pigmentation variation explained by previously associated or canonical pigmentation genes, and iii) novel pigmentation alleles contributing to variation in the ‡Khomani San and Nama populations. Results
We quantitatively phenotyped baseline skin color in 479 individuals (277 ‡Khomani, 202 Nama, Table S4) via narrow-band reflectometry to measure hemoglobin and melanin of both the left and right upper inner arms (STAR Methods), with M index = log10(1 / % red reflectance). We sequenced and/or genotyped a subset of phenotyped samples (Table S4, Methods). Skin pigmentation is lighter in the KhoeSan than the majority of other African populations, with baseline upper arm M index = 57.57 ± 10.12 (mean ± sd) in the ‡Khomani San. Baseline upper arm pigmentation in the Nama is slightly lower, with M index = 52.12 ± 8.93. The ‡Khomani are on average significantly darker than the Nama (p=3.6e-10, Figure 1C), but the variance is not significantly different (p>0.05). For comparison, we aggregated quantitative skin pigmentation across 32 globally diverse populations (4,712 individuals) assayed with a Derma Spectrometer (DSMI or DSMII) (Basu Mallick et al., 2013; Beleza et al., 2013; Candille et al., 2012; Coussens et al., 2015; Durazo-Arvizu et al., 2014; Edwards et al., 2010; Norton et al., 2006) (Figure 1A–B, Table S1). Only four African populations are available for comparison; among these only the Ghanians represent an equatorial African population with minimal recent admixture. Skin color is substantially darker in equatorial Ghanaians, where M index reaches a mean of 96.04 ± 10.94; M index for Cape Verdeans, who have ~40% European admixture on average, have slightly lighter (55.39 ± 13.00, p=5.6e-3) and considerably more variable pigmentation (p=1.9e-6) than the KhoeSan. Two other populations living in South Africa, the Xhosa and admixed Coloured populations, have respectively darker (M index=67.1±7.5) and similar (M index=53.1±8.5) pigmentation compared to the KhoeSan populations (Coussens et al., 2015).
Evidence of Increased Polygenicity in Skin Pigmentation Among Equatorial Populations We tested whether the correlation between absolute latitude and pigmentation was significant with our large, quantitatively phenotyped sample of global populations. As previously observed (Byard, 1981; Jablonski and Chaplin, 2010; Zaidi et al., 2017), we find that skin pigmentation is strongly associated with absolute latitude (R2=0.53, β=−1.18 on M index scale, p<2e-16); populations further from the equator have lighter skin pigmentation. We next tested whether variance in melanin within populations also varies across populations. Skin pigmentation has primarily been studied in lightly pigmented European and East Asian populations, where skin color varies minimally among individuals (Figure 1A–B). Less-studied equatorial and admixed populations, including Melanesians, Ghanaians, Cape Verdeans, South African admixed Coloured, and South Asians vary considerably more in skin pigmentation (Figure 1B). We find that absolute latitude is also significantly negatively associated with the standard deviation in melanin (R2=0.41, p=5.0e-5). Further, melanin distributions are heteroskedastic (i.e. the variance is not constant—rather, it changes over the range of observed M index), with the coefficient of variation, a standardized metric of phenotypic dispersion, decreasing with increasing distance from the equator (cv=σ/μ, R2=0.14, p=0.03, Table S1).
A sign test comparing variances in lighter versus darker population pairs within the same study indicates that populations with lighter skin have significantly reduced phenotypic variance than expected by chance (p=2.01e-8). These results suggest that there is reduced genetic heterogeneity and/or reduced variance in the population distribution of causal effect sizes contributing to lighter versus darker pigmentation. There is more than an order of magnitude difference in variance between the lightest and darkest populations (i.e. Irish vs Ghanaian F=0.03, p=6.7e-23). Europeans and East Asians have significantly less variation than South Asians (F=0.25, p=1.06e-14 and F=0.30, p=1.27e-10, respectively, Figure 1B). Cape Verdeans with the highest quartile of European admixture have lighter, less variable skin color than individuals with the lowest quartile of European ancestry (p=4.28e-9, although notably ancestry proportions are bimodal across individuals). Among Melanesians, islands at similar latitudes with more lightly pigmented individuals on average show less variance than those with more darkly pigmented individuals (e.g. one-sided F test comparing variance among more lightly pigmented New Britain individuals versus individuals from Bougainville, p=2.89e-9, Figure 1B). Among the ‡Khomani and Nama, comparing individuals with primarily European admixture (>20%, N=124) to individuals with primarily Bantu admixture (>20%, N=91), we find significantly greater melanin variation among KhoeSan individuals with more Bantu admixture (p=1.33e-4).
Ancestry and Skin Pigmentation Variation in the KhoeSan The ‡Khomani San and the Nama have both experienced admixture with neighboring darker-skinned Bantu-speaking groups beginning ~450 years ago, as well as with lighter-skinned European settlers who first arrived in the Northern Cape during the late 18th century (Uren et al., 2016a). We assessed these ancestry proportions using unsupervised allele frequency clustering with ADMIXTURE as well as principal components analysis (PCA, STAR Methods). At k=3, we observe distinct clustering between Europeans, Bantu-speaking and West African populations, and KhoeSan populations; both the Nama and the ‡Khomani have ~75–80% KhoeSan-specific ancestry. For k=7, which gives most stable ancestry estimates, we observe a partitioning of the KhoeSan ancestry into ‘northern Kalahari’ ancestry shared with Ju|’hoansi and a distinct southern or circum-Kalahari ancestry present in the Nama and the ‡Khomani. On average, in the ‡Khomani San we find 55% northern Kalahari KhoeSan ancestry, 21% southern Kalahari KhoeSan ancestry, 11% European ancestry (common in CEU and French individuals), 12% western African ancestry (common in Yoruba and Bantu-speaking populations), and 2% attributable to other African populations (Tanzanian hunter-gatherers, East African, and North African populations, Table S2, Figure 2A and Figure S2A). The Nama differ from the ‡Khomani in their proportion of northern versus southern Kalahari ancestry; they have 17% northern Kalahari ancestry, 62% southern Kalahari ancestry, 9% European ancestry, 10% western African ancestry, and 1% attributable to other African populations on average. The western African fraction in the Nama is significantly more variable among individuals (p=1.08e-5), resulting from recent Damara gene flow (Uren et al., 2016a). The partition of ancestry components occurs in the same order and is correlated between ADMIXTURE and PCA (Figure 2, Figure S2A,D–F).
In a multivariate mixed model with the significant European and Bantu admixture components, European and Bantu ancestry are strongly correlated with light (β = −18.09, p=2.9e-03) and dark skin (β = 25.60, p=1.8e-09), respectively. Together, we estimate that fixed admixture effects explained 34% of the variation in skin color (adjusted R2); by comparison, 44% of pigmentation variation in Cape Verdeans is explained by admixture effects (Beleza et al., 2013). Marginal associations are shown in Figure 2B, with pairwise ancestry correlations shown in Figure S2B. Southern Kalahari ancestry frequent in the Nama is significantly anti-correlated with Bantu ancestry and is marginally predicted to lighten skin, but not when modeled jointly with Bantu ancestry in a multivariate model. Interestingly, the mean pigmentation of Nama and ‡Khomani individuals with <90% KhoeSan ancestry is not significantly different from individuals with >90% KhoeSan ancestry (p=0.94), although the variance is significantly greater in more admixed individuals (admixture from either/both European or Bantu ancestries, p=2.2e-3). These results suggest that while admixture increases phenotypic variance, pigmentation alleles on KhoeSan haplotypes contribute more to the overall heterogeneity than those on European or Bantu haplotypes. Consistent with this result, we observe substantial skin pigmentation variation among related individuals, which, coupled with high heritability (see below) suggests a role for large effect sizes of alleles contributing to pigmentation…
A Complex Genetic Architecture in the KhoeSan The genetic architecture of skin pigmentation has been described as simpler than many other phenotypes, for which only a few genes explain ~35% of the total variation in a given population, and average genomic ancestry explains an additional ~44% of the variation, indicating a long tail of smaller effects (Beleza et al., 2013; Candille et al., 2012). We investigated how much of the heritable variation in KhoeSan populations can be ascribed to previously annotated pigmentation gene sets (Figure 3A). The first gene set (GS1) consists of 14 genes containing or near previously discovered skin pigmentation genetic associations in Europeans, East Asians, Cape Verdeans, and Native Americans (Table 2 and Table S6A). The larger, second gene set (GS2) contains 50 genes compiled previously (Beleza et al., 2013) from human pigmentation associations, positive selection scans, and model organism pigmentation loci. The third gene set (GS3) contained 50 loci most significantly associated with pigmentation in the KhoeSan (phase 1, see novel variants section below). We partitioned the genome into GS1, GS2, GS3, and the rest of the genome and performed four comparisons, computing the variance explained by: GS1 versus the rest of the genome, GS2 versus the rest of the genome, GS3 versus the rest of the genome, and GS1 versus GS2 versus the rest of the genome. For each comparison, we performed a restricted likelihood ratio test. The GS1 and GS2 gene sets do not explain a significant fraction of the heritability; that is, the heritability estimates overlap with zero. Rather, the remainder of the genome explains the overwhelming majority of the heritability (Figure 3B, σ2GS1=0.08 vs σ2Genome=0.82, pGenome=2.7e-5; σ2GS2=0.09 vs σ2Genome=0.79, pGenome=3.3e-4; and σ2GS1=0.08 vs σ2GS2=0.09 vs σ2Genome=0.71, pGenome=2.5e-3, respectively). This result contrasts with conclusions from previous studies and indicates that the vast majority of variation in KhoeSan skin pigmentation arises from pigmentation genes yet to be discovered, providing strong evidence for a complex, polygenic architecture. GS3 explains a small but significant fraction of the heritability, as discussed below.
Discussion Pigmentation has been described previously as a relatively simple trait with few loci of large effect contributing to the phenotype (Sulem et al., 2007; Walsh et al., 2013). However, populations living in continental Africa, where humans have the greatest genetic diversity and pigmentation variability, have been largely ignored in genetic studies with quantitative phenotypes. We investigated the genetic architecture of pigmentation in two KhoeSan populations: the ‡Khomani San and Nama, where baseline melanin variation is substantial. Southern African KhoeSan populations are the most polymorphic modern human populations yet studied (Henn et al., 2011), and provide a unique glimpse into the evolution of pigmentation. Novel Genetic Associations with Pigmentation We have performed the first genetic discovery effort for pigmentation loci in the Nama and ‡Khomani San populations. The strongest allelic associations include previously associated variants, noncoding regions near canonical pigmentation genes, and novel genes shown in model organisms to have a role in pigmentation. The strongest association is in SLC24A5, which is a well-known pigmentation gene (Lamason, 2005) and is among the most differentiated regions of the genome between European and African populations–indicative of strong positive selection in northern Europeans (Sturm and Duffy, 2012). We find that derived variants in SLC24A5 are at high frequency in the KhoeSan, including missense mutations that influence skin and eye pigmentation (Table 2). Notably, these variants are segregating at higher frequency than expected by recent European admixture alone. Three possible evolutionary scenarios that may explain these elevated frequencies are: 1) these variants arose in southern Africa more than 100,000 years ago and were later selected for in Europeans after the out-of-Africa migration in response to northern UVR environments. Alternatively, 2) these variants arose in Europe/Near East, were introduced into KhoeSan populations via “back to Africa” migration into southern Africa predating 17th century European colonialism (Pickrell et al., 2014; Uren et al., 2016a), and have since been positively selected in the KhoeSan. Lastly, 3) a recurrent mutation (G to A transition at the CpG ancestral dinucleotide, a class of mutations shown to have elevated mutation rates) occurred. Considerable future work is needed to definitively disentangle these scenarios.
The Polygenic Architecture of Pigmentation in Africa We assessed the heritability of baseline skin pigmentation, and find that it is virtually completely heritable in our KhoeSan sample. In contrast, tanning status is primarily environmental, with heritability estimates which are not significantly different from zero. In European populations, predictive models based on only 9 SNPs capture up to 16% of the variance in skin pigmentation (Liu et al., 2015), highlighting its relative simplicity. We applied a predictive model based on these SNPs to the Nama and ‡Khomani San populations, and find no significant association between predicted skin color and spectrophotometrically measured skin M index, showing that this estimation fails to capture the genetic variation driving the phenotype in the KhoeSan. Given the large effect sizes and high fraction of variation explained in Eurasian populations, we asked whether and how much of the phenotypic variation can be explained by previously identified genes. All gene sets, including previously associated loci, canonical pigmentation genes, and the most significantly associated variants in this study, explained a small fraction of the phenotypic variance (σ2GS1=0.08, σ2GS2=0.09, σ2GS3=0.23, respectively). As expected from previous work (Martin et al., 2017), our results indicate that genetic risk prediction is strongly affected by population structure. Most of the pigmentation variability in KhoeSan populations is not explained by previously identified loci, suggesting that more than 50 loci (and indeed, likely far more, given our genomic heritability estimates) with a distribution of mostly small effects contribute to variation in pigmentation in the KhoeSan. This suggests that skin pigmentation is a far more complex trait than previously discussed, analogous to numerous other complex traits discussed in biomedical literature
The Evolution of Skin Pigmentation: Selection and Constraint By aggregating a large set of quantitative skin pigmentation phenotypes (N=4,712) from globally diverse populations, we have demonstrated heteroskedasticity as a function of latitude. As observed previously, we find a strong correlation between absolute latitude and average skin pigmentation reflectance caused by melanin content. We also observe that populations with lighter skin have reduced variation within any given study: populations furthest from the equator have narrower distributions, while populations closest to the equator have wider distributions. These patterns suggest that selection is acting differently at different latitudes. In equatorial regions, strong directional selection for darker pigmentation has shifted the distribution means in some populations to M indices greater than 90, but with wide variances. This is consistent with a ‘threshold’ model (Chaplin, 2004) in which the protective benefit of melanin needs to meet some minimum threshold but with no penalty to darker pigmentation; alternatively, diversifying selection could maintain the wide variance. In stark contrast, pigmentation in far northern European and Asian populations has been under directional selection for decreased melanin production, reflected by very narrow distributions. There may be biological constraints on the lower boundary of skin pigmentation, and/or due to the strong positive selection acting on a few large-effect alleles, there is little genetic variability left at these pigmentation loci. This would simplify the genomic architecture, with relatively few alleles of large effect driving the phenotype, particularly alleles that lighten skin at extreme northern latitudes, and could explain why prior investigations observed an almost Mendelian inheritance of large effect light pigmentation alleles.
Finally, populations at intermediate latitudes have increased variance and higher means than populations in northern Eurasia, but less than equatorial populations. The most parsimonious explanation for this pattern is that stabilizing selection affects the light and dark tails of the pigmentation distribution (Barton, 1999). The Nama and ‡Khomani San appear to be two such instances of this intermediate variation within Africa, likely attributable to their geographic distance from the equator in far southern Africa (~24–29 degrees South). The observed mean and variance differences across the full spectrum of skin pigmentation by latitude may be driven by imbalanced opposing adaptive pressures, where selective forces to produce vitamin D and protect folate from photolysis are unequal and change in response to UV radiation exposure. Given our heritability results and the observed variability in baseline pigmentation; light skin pigmentation in the KhoeSan appears to be due to a combination of many small-effect mutations as well as some large-effect variants. The evolution of the pigmentation phenotype in these populations cannot be explained in terms of only a few variants segregating in Eurasians. A fuller characterization of the genes underlying the architecture in Africans is needed before we can distinguish between the hypothesis of directional versus stabilizing selection across different latitudes (Berg and Coop, 2014).
Conclusion Because African populations often carry the ancestral (i.e. dark) allele for skin pigmentation genes identified in Eurasians, allusions to African skin pigmentation have ignored the great variability in this phenotype across Africa. Here, we reiterate that skin pigmentation varies more in Africa than any other continent, and we show that pigmentation in African populations cannot simply be explained by the small number of large effect alleles discovered in Eurasians. Even in light to moderately pigmented KhoeSan populations, the polygenicity of skin pigmentation is much greater than Eurasians, encompassing both known pigmentation genes as well as novel loci. We argue that the distributions of skin pigmentation globally suggest different forces of selection operating at various latitudes. To better understand baseline pigmentation, one of the most rapidly-evolving traits and strongest cases for positive selection in humans, it is essential to quantitatively measure and study pigmentation in a large set of genetically diverged populations that have historically been exposed to different levels of UV radiation. As human genetics moves to ever larger studies of complex traits, the full picture of genetic architecture will remain incomplete without representation from diverse worldwide populations.
-------------------- Mahirap gisingin ang nagtutulog-tulugan. Posts: 26239 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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As for Khoisan ancestry itself. The fallacy that they have significant Eurasian ancestry came from the 2015 Mota study ERROR that unfortunately yet unsurprisingly many Euronuts are still touting. Yet the fallacy totally contradicts the countless ancestry studies on Khoisan showing that they have nil Eurasian ancestry and that the only Khoisan with significant Eurasian ancestry are the Cape Coloureds, that is descendants of Khoisan peoples in the coasts that intermarried with European colonizers.
This is seen in the 2013 study below:
Complex Patterns of Genomic Admixture within Southern Africa Abstract Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly proportional to geographic distance. The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion) and inter-continental migration (European-driven colonization) have resulted in complex patterns of admixture between ancient geographically isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan representation, we identify the Ju/'hoan (n = 19) as a distinct early diverging human lineage with little to no significant non-Khoesan contribution. In contrast to the Ju/'hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15) and Khoesan !Xun (n = 14), respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan contributions to the Coloured (n = 25) and Baster (n = 30) populations. The latter populations were further impacted by 170 years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation (admixture). The populations of southern Africa provide a unique opportunity to investigate the genomic variability from some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently diverged human lineages.
Author Summary The Khoesan have received recent attention, as they are the most genetically diverse contemporary human populations. However, Khoesan populations are poorly defined, while archeological evidence suggests a once broader dispersal of click-speaking southern African foragers. Migrations into the regions populated by contemporary Khoesan involved agro-pastoral Bantu around 1,500 years ago, followed over a millennium later by the arrival of European colonists establishing a halfway station for a maritime route between Europe and the East, which led to unions between diverse global populations. Using almost a million genetic markers for 103 individuals, we confirmed a significant Khoesan contribution to five southern African populations. The Ju/'hoan show genetic isolation (early divergence from all other modern humans), carry no significant non-Khoesan contributions, and unlike most global populations lack signatures of gene-based adaption to agriculture. The !Xun show two distinct Khoesan prehistories; while comparable to the female-derived Khoesan contribution to the amaXhosa Bantu, the male-derived Bantu contribution to the !Xun most likely represents cultural-driven gender-biased gene-flow. Emanating largely from male-derived European ancestral contributions, the Basters showed the highest maternal Khoesan contribution, while the Coloured showed the largest within population and regional-associated variability. The unique admixture fractions of the two latter populations reflect both early diverged and recently diverged human lineages.
quote:Originally posted by Djehuti: As for Khoisan ancestry itself. The fallacy that they have significant Eurasian ancestry came from the 2015 Mota study ERROR that unfortunately yet unsurprisingly many Euronuts are still touting.
I agree with your larger point that Khoisan peoples likely evolved at least some of their depigmentation independently, but don't they carry at least one genetic allele of West Eurasian origin that causes lighter skin?
Mind you, one allele would not necessarily require the Eurasian component in Khoisan ancestry to be very large. It could have become widespread among the Khoisan due to selection even without the autosomal input being large.
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Wasn't there a study back in either 2017 or 2018 that showed that the light skin allele of the Khoisan was indignous?
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Tazarah
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That's funny. There is a notorious euronut on this very website who tried to use the "khoisan light skin came from eurasians" argument against me.
Rofl. Pseudos gonna pseudo
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Tukuler
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Since quite a few have colonial and neo-colonial European ancestors, who either were attracted to local females --think of Saartjie Baartman (link) the European whiteman's original big butt fetish-- or else had no other sexual outlet, why wouldn't such ones harbour all kinds of Eurasian genes? I do wonder where their far east Asian genes came from though. See Pickerell (2012), Schuenemann (2017).
Could their Chinese genetics be of the same source found in Swahili coastals/islanders? I mean the great Cinese explorers sailing centuries ago like
Remember high culture medieval SE Africans had what today are SW African click speaker as well as baNtu genetics.
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^ It is possible. East Africans have had maritime contact via the Indian Ocean trade from antiquity through the Middle Ages from the kingdom of Azania to the Kilwa Sultanate and Great Zimbabwe. Some of the Cape Coloured folk definitely have recent South Asian ancestry but if one were to judge by the Admixture analysis especially when considering the Khomani, I'd say more than likely they carry traces of some pre-OOA ancestry.
quote:Originally posted by the lioness,:
Yes, I think natural selection plays a large part as well since Southern Africa's temperate zone is essentially 'Mediterranean' just like North Africa is, meaning that the environment no longer had any pressure for as high melanin content as equatorial regions the same as North Africa.
quote:Originally posted by BrandonP: I agree with your larger point that Khoisan peoples likely evolved at least some of their depigmentation independently, but don't they carry at least one genetic allele of West Eurasian origin that causes lighter skin?
Mind you, one allele would not necessarily require the Eurasian component in Khoisan ancestry to be very large. It could have become widespread among the Khoisan due to selection even without the autosomal input being large.
That's the problem. Unlike North Africans who show significant Eurasian influence the Khoisan show very little which is confined to coastal areas of European contact. Even if there is evidence of Eurasian influence via pastoralists from the northeast, it still doesn't explain why light skin is prevalent among remote hunter-gatherers yet Northeast Africans who have higher frequencies of Eurasian admixture are darker still.
In fact, I've always questioned just how Eurasian is the SLC24A5 gene and for good reason.
Pigmentary Diversity: Identifying the genes causing human diversity SLC24A5 has a striking pattern of variation in human populations. A coding variant in the gene has previously been described as one of a set of ancestry-informative markers. The ancestral form encodes alanine at residue 111, whereas a derived allele encodes threonine. Alanine is present at this position in all known members of the SLC24 subfamily of proteins, suggesting the change to threonine has functional consequences. The derived variant is universally present on all European chromosomes analysed, while chromosomes of *African* and Asian origin almost invariably carry the ancestral form. The population difference puts this variant in the top 0.01% of all variants studied. Furthermore, analysis of the HapMap Consortium data6 found that SLC24A5 was within a chromosomal region that has a striking reduction of heterozygosity of SNPs in the European population. In fact, at 150 kb it is the longest such segment identified in the genome.1 Such a long conserved homozygous haplotype indicates that there has been strong selection on a gene or genes, which has swept this segment across the population, and selection for homozygosity eliminated recombination between SNPs, which maintained a long haplotype.
Another solute channel gene SLC45A2, or MATP, which is affected in human, mouse and fish pigmentary mutants, also shows strong association with ethnic ancestry. More than 90% of European chromosomes have a derived allele which is rare or absent in Africans. The small number of people of European descent with the ancestral form of the gene appear to have significantly more pigmented skin and there is clear evidence for a selective sweep of the chromosomal segment around the SLC45A2 in the European population.
quote:Originally posted by Askia_The_Great: Wasn't there a study back in either 2017 or 2018 that showed that the light skin allele of the Khoisan was indignous?
Yeah, you're probably referring to the 2018 Benna Henn I cited in the opening post. LOL
quote:Originally posted by Tazarah: That's funny. There is a notorious euronut on this very website who tried to use the "khoisan light skin came from eurasians" argument against me.
Rofl. Pseudos gonna pseudo
And nuts are nutty, which is why I prefer to throw facts even if it goes over their heads.
Posts: 26239 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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And as a person who has been to South Africa twice and going back there again, the western cape DEFINIETLY does have a "Mediterranean" like climate. I can 100% confirm. Been to Cape Town, and it was like a southern California in Africa lmao.
And I strongly doubt that most of the Khoisan light skin is due to recent admixture with non-Africans or Eurasians. Because if that's the case then the majority of Bantu Southern Africans have that admixture too, because Khoisan admixture/characteristics is STRONGLY seen in southern Africans, and no not just the Xhosa but they do have the biggest influence. I seen Lesothos, Tswanas, and few others.
Posts: 1891 | From: NY | Registered: Sep 2014
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^ People forget just how ancient and thus genetically diverse the Khoisan are. Here is a recent study from 2017:
Ancient Genomes from Southern Africa Pushes Modern Human Divergence Beyond 260,000 years ago ABSTRACT Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years 35 ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago,including the Ju|’hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) ‘hot spot’ for the evolution of our species.
And not many people realize that although they are small minority today they were actually a much larger population in the past.:
Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history Abstract The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/’hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100–150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80–100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.
Genetic origins of southern African individuals In order to examine the genetic ancestries of the six individuals, we applied ADMIXTURE11 and EIGENSOFT12 to the genotyping data set of 419,969 nuclear single-nucleotide polymorphism (SNP) genotypes from 1,448 worldwide individuals along with genotypes extracted from the 14 genome sequences for the same SNP loci (Supplementary Table 1). Figure 1 shows the results for selected populations, emphasizing our six individuals. Entire results are shown in Supplementary Figs 1–3. On the basis of the ADMIXTURE result, Khoisan populations include two different ancestries, northern Khoisan and southern Khoisan, with evidence of past gene flow within the Khoisan and/or between the Khoisan and non-Khoisan, except for the Ju/’hoansi population (Fig. 1a). Individuals NB1 and NB8 belong to the Ju/’hoansi (Fig. 1c) and appear to have only northern Khoisan ancestry (Fig. 1b). We also applied a different method13, which uses linkage disequilibrium decay, to detect admixture between the Ju/’hoansi and other populations and show the result in Supplementary Fig. 7.
What's fascinating is that the great genetic divergence of Khoisan from other Africans let alone non-Africans as well as the secondary split between Northern Khoisan and Southern Khoisan is reflected in other genetic findings...
But you are correct that Bantu speakers upon their immigration into the region absorbed and assimilated Khoisan speakers and that even some Bantu languages like Xhosa preserve click word lexicon.
-------------------- Mahirap gisingin ang nagtutulog-tulugan. Posts: 26239 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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"Some"? Practically ALL Southern African(specifically South Africans, Batswana and Namibians) have click word lexicons.
Anyways good post. And not surprised that they had a larger population back then, however most would've been absorbed by arriving Bantu agriculturist. Also Im going to do some digging into northern vs southern Khoisan.
And yea, it actually been argued that Southern Africa being the origin of homo-sapiens. There is actually a cave with very ancient homo sapien skulls that I may check out.
Posts: 1891 | From: NY | Registered: Sep 2014
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Non-Africans tend to forget the Khoikhoi and the Saan are completely different ethnic groups varying in culture and economy.
The one recognize personal property wealth, the other are 'egalitarian' in that regard. The one are pastoral since 2000 years ago having herds acquired from or brought with them from further east and north. The other are quite nomadic foraging hunters apparently since time immemorial.
Although both are 'red people' in the eyes of baNtu speakers, the Khoikhoi herdsmen were the ones European invaders had intercourse with, they and the Indonesians they enslaved and shipped to southernmost Africa. The mobile pre-metal Saan were less attractive to baNtu, Arab/Iranians, European s, Indonesians, and Indians alike. Or maybe just much harder to get ahold of
Just as Khoikhoi women are noted for their 'cockscombs', Saan men have 90° angled penii in the rock art.
posted
^ The Khoisan not only have golden or yellowish complexions but epicanthic eye folds with fatty deposits in the eye-sockets that they share in common with so-called "Mongoloids" of East Asia.
Khoisan also have the tightest coiled hair of all Africans even more coiled than the stereotypical 'kinky' hair, and they not only possess some of the highest frequencies of steatopygia (fat booty) but the maximum or extreme form of steatopygia where the buttocks in woman is like a hump! This lead to the exhibition exploitation of Khoisan women more than other African women especially Sarah Bartman.
bushman
Sarah Bartman a.k.a. 'Hottentot Venus'
quote:Originally posted by Ebony Allen: Djehuti, if you don't mind me asking how old are you?
I'm in my late 30s. Why?
-------------------- Mahirap gisingin ang nagtutulog-tulugan. Posts: 26239 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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I was just curious. You've been on this forum a long time. I honestly thought you were older than that.
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^ I've been a member of this forum since high school. So yeah, it's been a long time!
Posts: 26239 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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I'm a few years younger than DJ since I will turn 33 next month, but I've been here since my last year of middle school. So you could say I am one of the longest-staying veterans.
quote:Originally posted by Djehuti: ^ The Khoisan not only have golden or yellowish complexions but epicanthic eye folds with fatty deposits in the eye-sockets that they share in common with so-called "Mongoloids" of East Asia.
Khoisan also have the tightest coiled hair of all Africans even more coiled than the stereotypical 'kinky' hair, and they not only possess some of the highest frequencies of steatopygia (fat booty) but the maximum or extreme form of steatopygia where the buttocks in woman is like a hump! This lead to the exhibition exploitation of Khoisan women more than other African women especially Sarah Bartman.
All three traits which also influenced southern African Bantu population. The epicanthic eye folds, very coiled hair(which is why many SAns can't grow their hair long), and big buttocks? Definitely, especially with the women lol. Southern Africans(Namibians, Batswana, South Africans, Lesothos) are really just admixed Khoisans. Similar to how East African Bantus especially in the great lakes have Nilotic and Cushite admixture.
Posts: 1891 | From: NY | Registered: Sep 2014
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quote:Originally posted by Tukuler: Non-Africans tend to forget the Khoikhoi and the Saan are completely different ethnic groups varying in culture and economy.
The one recognize personal property wealth, the other are 'egalitarian' in that regard. The one are pastoral since 2000 years ago having herds acquired from or brought with them from further east and north. The other are quite nomadic foraging hunters apparently since time immemorial.
Although both are 'red people' in the eyes of baNtu speakers, the Khoikhoi herdsmen were the ones European invaders had intercourse with, they and the Indonesians they enslaved and shipped to southernmost Africa. The mobile pre-metal Saan were less attractive to baNtu, Arab/Iranians, European s, Indonesians, and Indians alike. Or maybe just much harder to get ahold of
Just as Khoikhoi women are noted for their 'cockscombs', Saan men have 90° angled penii in the rock art.
Like I said I been to South Africa twice, and I am not doubting admixed Khoisan people(I know how they look like and they live modernly), but using this argument then Southern African Bantus as a WHOLE have significant Eurasian admixture. If I'm reading your post right. But if I am, then recent European intercourse with Khoisans is irrelevant to explain their features, especially the Khoisan man Lioness posted.
The Khoisan traits that Djehuti lists can all be found in Bantu South Africans. I'm going to post eye candy for an example(I prefer eye candy lol).
Ignore the makeup and weave. Eyes and yellowbone like skin complexion screams Khoi influence. You see many like her walking around Johannessburg lol.
Edit:
Most mixed Khoisans are listed/grouped as Coloureds and are integrated with the Coloured community.
Edit:
This would be a better example of a admixed Khoisan group. Nama girls, and even still we don't know for sure. Posts: 1891 | From: NY | Registered: Sep 2014
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
This is not something new for me. My library lost around 2003 had books on Saan, some were profusely illustrated. Then there were physical anthropology and ethnology books by Keane and others like * The Secret Museum of Mankind * Women of All Nations * The Living Races of Mankind etc. thankfully now available to me again via the Web. Not to mention racial anthropologists like Coon, and disciple Baker, who promoted a distinct Capoid/Sanid race. Would you believe there are, by definition, pseudo-epicanthic folds not taxonomically identical to the East Asian epicanthic fold?
Minutely compare Mandela's eyefold to this Korean girl's eyefold, especially her definitive eye corner near the nose. Careful observation proves they just are not the same as I was taught in university. If the Asian has the 'true epicanthic fold' then Africans have a 'pseudo epicanthic fold' per accepted taxonomy. I'd just reference the one the African epicanthic and the other the Asian epicanthic without resort to technical definition.
I just suggest finding and looking at ADMIXTURE graphs that include Khoikhoi, Saan, Coloureds, and baNtu to understand my point which has nothing at all to do with supporting any idea or concept that Click speakers significantly descend from or get much of any of their physical characteristics from any pre-modern Eurasian admixture.
Redux Gurdasani (2014) Extended Data Figure 6
Redux Schuenemann (2017) Supplementary Fig. 4
Redux Choudhury (2020) Fig. 2a
In Baker (2017) Figure 1 various Khoikhoi, Saan, Basters and Coloureds reveal distinct clustering
I solicit precisions when backed by books, reports, articles, etc., drawn from published professionals of the related field. I'm not into debate or chat. I will gladly answer any questions of clarity on what I actually posted and said when and only when a direct quote by me is supplied.
quote:Originally posted by the lioness,: [QB] Epicanthic folds appear in East Asians, Southeast Asians, Central Asians, North Asians, some South Asians, Polynesians, Micronesians, Indigenous Americans (as well as Mestizos), the Khoisan, Malagasy, occasionally Europeans (e.g., Scandinavians, Hungarians, Samis, Irish and Poles) and among Nilotes.
Epicanthal folds are oblique or vertical folds from the upper or lower eyelids towards the medial canthus. Usually bilateral, they may involve both the upper and lower eyelids. These folds are caused by excessive development of the skin across the bridge of the nose.
There are 4 types of epicanthus:
a) Epicanthus superciliaris: fold originates from the brow and follows down to the lacrimal sac b) Epicanthus palpebralis: involves both upper and lower eyelids c) Epicanthus tarsalis: fold most prominent along upper eyelid d) Epicanthus inversus: most prominent along lower eyelid
Epicanthic folds
^^notice in each case the Epicanthic folds is affecting the inner corner of the eye
.
However there is another eye type called "hooded eye" or "droopy eye" "baggy eye" "puffy eye", the medical term Ptosis and Dermatochalasis, this droop occurring more toward the outer corner Ptosis is caused by a weakening of muscle that results in the upper eyelid drooping over the eye. Whereas, Dermatochalasis sometimes called baggy eyes, is caused by excess skin, fat, or muscle in the eyelid area. Both conditions cause a similar appearance
top row, middle "hooded" instead of the fold affecting the inner corner of the eye the slope is going down toward the outer outer corner (and in some cases goes over it)
the outer corner is showing but the droop comes in toward the outer corner. Sometimes caused by ageing but not always. Dermatochalasis is a medical term describing excess skin along or around the upper and/or lower eyelid areas. Below an example affecting the upper lid (but not the lower)
hooded eye(top) ("droopy eye")
non-hooded eye (bottom)
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What I observe in Khoe and San people is more in the realm of a hooded eye, Dermatochalasis rather than an Epicanthic fold, but I could be wrong
If you look at different Khoe or San people you see some variation. You might says he has some Epicanthal fold but also a prominent "hoody eye" a puffiness, a bulge in this case. His eyelid at the top looks like is is merged as one form into his brow ridge. This is going over the top lid There are two things but look like one single bulge here. This could be protective against sand storms
Another thing I have noticed in some videos is that their skin color varies but the lighter type resembles a sand color, that would be an advantage for a hunter, to blend into the background more at a distance
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quote:Originally posted by BrandonP: I'm a few years younger than DJ since I will turn 33 next month, but I've been here since my last year of middle school. So you could say I am one of the longest-staying veterans.
You and I were born the same year. I'm already 33.
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This discussion is much more complex as a lot of the identities in Africa today are bound by or influenced by colonial histories. And this has caused a lot of confusion or conflict across many groups because of the difference between how Africans viewed themselves based on culture and language vs the European view based on race and other constructs.
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