The timing of pigmentation lightening in Europeans
Open accessAbstract
The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin to facilitate vitamin D synthesis in regions far from the equator. Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color. However, little work has focused on estimating the time frame over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes. To provide a temporal framework for the evolution of lighter pigmentation, we used forward Monte Carlo simulations coupled with a rejection sampling algorithm to estimate the time of onset of selective sweeps and selection coefficients at four genes associated with this trait in Europeans: KITLG, TYRP1, SLC24A5, and SLC45A2. Using compound haplotype systems consisting of rapidly evolving microsatellites linked to one single-nucleotide polymorphism in each gene, we estimate that the onset of the sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration, whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000-19,000 years, well after the first migrations of modern humans into Europe. We suggest that these patterns were influenced by recent increases in size of human populations, which favored the accumulation of advantageous variants at different loci.
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Claims the paper makes
28 of 79 cited sources checked · 13 supported · 1 flagged · accuracy not yet measured
- Premisecitation
The levels of UVR required to synthesize vitamin D are higher in individuals with darker skin.
“Because the levels of UVR required to synthesize vitamin D are known to be higher in individuals with darker skin (Holick 2003;Chen et al. 2007)”
Quote in the paperSubstantial claim1 of 2 sources checked - Premisecitation
Lack of knowledge about the genetic basis of natural variation in skin pigmentation has prevented the evaluation at the molecular level of the role played by natural selection in shaping the variation of this complex phenotype among human populations.
“However, lack of knowledge about the genetic basis of natural variation in skin pigmentation has prevented the evaluation at the molecular level of the role played by natural selection in shaping the variation of this complex phenotype among human populations (Parra 2007).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Parra 2007 source
The Introduction (page unavailable) says researchers were only beginning to understand the genetic basis of normal pigmentation variation. But the section on detecting signatures of selection (page unavailable) describes molecular tests and studies identifying pigmentation candidate genes under selection. The paper supports a historical knowledge gap, not the unqualified claim that it prevented molecular evaluation. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premisecitation
Previous studies using several population samples from different continents have shown that, unlike SLC45A2, derived alleles at SLC24A5, TYRP1, and KITLG are present at low frequencies in some sub-Saharan populations.
“Previous studies using several population samples from different continents have shown that, unlike SLC45A2, derived alleles at SLC24A5, TYRP1, and KITLG are present at low frequencies in some sub-Saharan populations (table 1, see also Yuasa et al. 2006;Frazer et al. 2007;Norton et al. 2007;Soejima and Koda 2007;Coop et al. 2009;Pickrell et al. 2009).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites Yuasa et al. 2006 source
- cites Frazer et al. 2007 source
The Natural selection section discusses derived-allele frequencies across SNPs generally, and the Advances made possible by the Phase I haplotype map section identifies geographically diverse samples. Neither reports low-frequency derived alleles at SLC24A5, TYRP1, or KITLG in sub-Saharan populations or contrasts them with SLC45A2 (searched those gene names and pigmentation-related allele frequencies). (LLM, conf=0.72)
Experimental — accuracy not yet measured - cites Norton et al. 2007 source
- Findingcitation
The SNP-haplotype structure around the derived alleles at all loci bears signals of Eurasian hard sweeps that are not expected under selection from standing variation.
“In any case, the SNP-haplotype structure around the derived alleles at all loci bear signals of Eurasian hard sweeps that are not expected under selection from standing variation (Hermisson and Pennings 2005;Izagirre et al. 2006;McEvoy et al. 2006;Soejima et al. 2006;Voight et al. 2006;Lao et al. 2007;Myles et al. 2007;Norton et al. 2007;Sabeti et al. 2007;Williamson et al. 2007;Pickrell et al. 2”
Quote in the paperSubstantial claim2 of 3 sources checked- cites Hermisson and Pennings 2005 source
The Abstract and “Footprints of soft sweeps” section distinguish hard sweeps from soft sweeps that can arise from standing variation, and describe their different haplotype patterns. The paper does not examine the cited Eurasian loci or establish that all show hard-sweep signals. It also says standing variation may produce a soft sweep, not that a hard-sweep pattern is categorically impossible under selection from standing variation. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites Izagirre et al. 2006 source
The EHH Test section reports haplotype-based signatures of recent positive selection at two loci in Caucasians, TYRP1 and SLC24A5. It does not establish such signals at all loci or across Eurasian populations: three other significant loci showed signals only in Yorubans. The passages do not distinguish hard sweeps from selection on standing variation. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites McEvoy et al. 2006 source
- Interpretationcitation
Different genes are responsible for the reduction of melanin content in Europeans and East Asians.
“suggesting that different genes are responsible for the reduction of melanin content in Europeans and East Asians (McEvoy et al. 2006;Lao et al. 2007;Myles et al. 2007;Norton et al. 2007;Pickrell et al. 2009).”
Quote in the paperNot a substantial claim1 of 3 sources checked
- Premisecitation
Different skin lightening alleles at OCA2 have likely experienced independent sweeps in Europeans and East Asians.
“Additional evidence for convergent adaptation is provided by genes such as OCA2, in which different skin lightening alleles have likely experienced independent sweeps in Europeans and East Asians (Lao et al. 2007;Edwards et al. 2010;Donnelly et al. 2011).”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites Lao et al. 2007 source
- cites Edwards et al. 2010 source
The Author Summary and Discussion state that different OCA2 alleles were selected in Europe and East Asia, consistent with independent evolution toward lighter pigmentation. But the Discussion identifies the selected European allele as a blue-eye allele; it does not establish that this allele lightens skin, as the claim specifies. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites Donnelly et al. 2011
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationcitation
The fact that the sweeps at SLC24A5, SLC45A2, and TYRP1 occurred well after the divergence of Europeans and East Asians increased the chance of convergent adaptation by shortening the delay between local adaptive mutations relative to the time necessary for advantageous variants to spread across Eurasia.
“Moreover, the fact that the sweeps at SLC24A5, SLC45A2, and TYRP1 occurred well after the divergence of Europeans and East Asians increased the chance of convergent adaptation by shortening the delay between local adaptive mutations relative to the time necessary for advantageous variants to spread across Eurasia (Ralph and Coop 2010).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Ralph and Coop 2010 source
Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
- Rests on an assumption: The four genes studied (KITLG, TYRP1, SLC24A5, SLC45A2) influence normal pigmentation variation.
- Premisecitation
Effective population size is one of the most important factors limiting the availability of adaptive mutations.
“As previously noted (Hawks et al. 2007;Karasov et al. 2010;Pritchard et al. 2010), effective population size is one of the most important factors limiting the availability of adaptive mutations.”
Quote in the paperSubstantial claim2 of 3 sources checked - Findingown data
The onset of the selective sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration.
“Using compound haplotype systems consisting of rapidly evolving microsatellites linked to one single-nucleotide polymorphism in each gene, we estimate that the onset of the sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration”
- Also stated in: § Introduction · hedged
“The modes of our age estimates indicate that the derived lineage shared by Europeans and East Asians at KITLG started to rise in frequency approximately 30,000 years ago, after the out-of-Africa migration”
- Also stated in: § Age and Selection Coefficient Estimates · hedged
“The modes for the age and selection intensity of KITLG sweeps using rs642742 estimated from European and Asian samples with the two models of inheritance were strikingly concordant (t 30,000-32,000 years; s 0.01-0.02;table 3).”
Quote in the paperSubstantial claim- The authors state this as an assumption: The haplotype combining the modal allele at each microsatellite locus represents the original haplotype.
- The authors state this as an assumption: Reverse mutation in microsatellites is negligible.
- The authors state this as an assumption: Fitness effects are additive or fully dominant.
- Also stated in: § Introduction · hedged
- Findingown data
The selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started within the last 11,000-19,000 years, well after the first migrations of modern humans into Europe.
“whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000-19,000 years, well after the first migrations of modern humans into Europe.”
- Also stated in: § Introduction · plain
“whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 occurred only within the last 11,000-19,000 years and not immediately after the first migrations of modern humans into Europe.”
Quote in the paperSubstantial claim- The authors state this as an assumption: The haplotype combining the modal allele at each microsatellite locus represents the original haplotype.
- The authors state this as an assumption: Reverse mutation in microsatellites is negligible.
- The authors state this as an assumption: Fitness effects are additive or fully dominant.
- Also stated in: § Introduction · plain
- Findingown data
Reconstructed SNP/microsatellite haplotypes show that derived alleles at TYRP1, SLC24A5 and SLC45A2 are associated with only subsets of possible haplotypes.
“The reconstructed SNP/microsatellite haplotypes clearly show that derived alleles at TYRP1, SLC24A5 and SLC45A2 are associated with only subsets of possible haplotypes (fig.2A-C and supplementary fig.S2, Supplementary Material online).”
Quote in the paperSubstantial claim - Findingown data
Coalescent-based tests failed to reject neutrality in all cases for KITLG.
“Our coalescent-based tests failed to reject neutrality in all cases”
Quote in the paperSubstantial claim - Findingown data
At the rs642742 SNP, the frequency of the KITLG*G derived allele in Africans is 7%, in contrast to high frequencies in Europeans and East Asians (80%).
“At the rs642742 SNP, the frequency of the KITLG*G derived allele in Africans is 7%, in contrast to the high frequencies found in Europeans and East Asians (80%).”
Quote in the paperSubstantial claim - Findingown data
Approximately 58% of chromosomes bearing the KITLG*G allele outside Africa are shared by Europeans and East Asians.
“Moreover, approximately 58% of chromosomes bearing the KITLG*G allele outside Africa are shared by Europeans and East Asians”
Quote in the paperSubstantial claim - Findingown data
Neutrality could not be rejected for SLC45A2 when intra-allelic diversity was measured by the average variance of repeat number (V) at linked microsatellite markers.
“However, neutrality could not be rejected for SLC45A2 when intra-allelic diversity was measured by the average variance of repeat number (V) at linked microsatellite markers (table 2).”
Quote in the paperSubstantial claim - Findingown data
For TYRP1, SLC24A5, and SLC45A2, the probabilities of observing two different haplotypes within derived alleles (HD) were consistently lower than expected under neutrality, irrespective of the demographic scenario.
“For TYRP1, SLC24A5, and SLC45A2, the probabilities of observing two different haplotypes within derived alleles (HD) were consistently lower than expected under neutrality, irrespectively of the demographic scenario (table 2).”
Quote in the paperSubstantial claim - Findingown data
KITLG displays more similar levels of intra-allelic diversity in ancestral and derived lineages than TYRP1, SLC24A5, and SLC45A2.
“In contrast with TYRP1, SLC24A5, and SLC45A2, KITLG displays more similar levels of intra-allelic diversity in ancestral and derived lineages (fig.2D and supplementary fig.S2, Supplementary Material online).”
Quote in the paperSubstantial claim - Findingcitation
The estimated selection intensity at SLC24A5 (s = 0.16 dominant, 0.08 additive) is considerably higher than at TYRP1 (s = 0.02-0.03) and SLC45A2 (s = 0.04-0.05).
“The intensity of selection estimated for the SLC24A5 locus, ranging from 0.16 in the dominant model to 0.08 under the more realistic additive model (Lamason et al. 2005), is considerably higher than at TYRP1 (s = 0.02-0.03)and SLC45A2 (s = 0.04-0.05).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Lamason et al. 2005 source
- Findingown data
The modes for age and selection intensity of KITLG sweeps using rs642742 estimated from European and Asian samples with the two models of inheritance were strikingly concordant (t 30,000-32,000 years; s 0.01-0.02).
“The modes for the age and selection intensity of KITLG sweeps using rs642742 estimated from European and Asian samples with the two models of inheritance were strikingly concordant (t 30,000-32,000 years; s 0.01-0.02;table 3).”
Quote in the paperSubstantial claim- The authors state this as an assumption: The haplotype combining the modal allele at each microsatellite locus represents the original haplotype.
- The authors state this as an assumption: Reverse mutation in microsatellites is negligible.
- The authors state this as an assumption: Fitness effects are additive or fully dominant.
- Findingown data
The modes of the age estimates at SLC24A5, TYRP1, and SLC45A2 are consistently found at 11,000-19,000 years under the dominant and additive fitness models.
“The modes of the age estimates at SLC24A5, TYRP1, and SLC45A2 are consistently found at 11,000-19,000 years, under the dominant and additive fitness models (table 3).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites table 3
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
Age calculations using alternative KITLG tag SNPs varied on average approximately 30% and 21% around estimates based on rs642742, assuming dominant and additive models, respectively.
“Age calculations using alternative KITLG tag SNPs varied on average approximately 30% and 21% around estimates based on rs642742 (supplementary table S3, Supplementary Material online), assuming dominant and additive models, respectively.”
Quote in the paperNot a substantial claim- The authors state this as an assumption: The haplotype combining the modal allele at each microsatellite locus represents the original haplotype.
- The authors state this as an assumption: Reverse mutation in microsatellites is negligible.
- The authors state this as an assumption: Fitness effects are additive or fully dominant.
- Findingcitation
Estimated selective coefficients at KITLG, SLC45A2, and SLC24A5 are consistent with their previously measured effects on skin pigmentation in admixed populations (2.8-3.8, 5, and 7.6-11.4 average melanin units, respectively).
“It is noteworthy that estimated selective coefficients at KITLG, SLC45A2, and SLC24A5 are consistent with their previously measured effects on skin pigmentation in admixed populations: 2.8-3.8, 5, and 7.6-11.4average melanin units at KITLG (Miller et al. 2007), SLC45A2 (Norton et al. 2007), and SLC24A5 (Lamason et al. 2005), respectively.”
Quote in the paperNot a substantial claim0 of 3 sources checked - Findingown data
Levels of intra-allelic diversity at the KITLG locus were compatible with neutrality for all demographic scenarios.
“Differently from TYRP1, SLC24A5, and SLC45A2, the levels of intra-allelic diversity at the KITLG locus were compatible with neutrality for all demographic scenarios”
Quote in the paperSubstantial claim - Findingown data
Haplotypes bearing the derived allele at TYRP1 and SLC24A5 tend to be more tightly clustered than at SLC45A2.
“Haplotypes bearing the derived allele at the TYRP1 and SLC24A5 loci (fig.2A and B) tend to be more tightly clustered than at the SLC45A2 gene (fig.2C), which displays a more interspersed pattern, probably due to early recombination between ancestral and derived lineages.”
Quote in the paperSubstantial claim - Findingcitation
Very few skin-lightening alleles are shared between Europeans and East Asians.
“the presence of very few skin-lightening alleles shared between Europeans and East Asians (McEvoy et al. 2006)”
Quote in the paperSubstantial claim0 of 1 sources checked- cites McEvoy et al. 2006 source
- Findingnone given
The geographic distribution of polymorphisms at SLC24A5, SLC45A2, and TYRP1 is primarily restricted to European populations.
“the three genes in which the geographic distribution of the polymorphisms is primarily restricted to European populations”
Quote in the paperSubstantial claim0 of 1 sources checked- cites table 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationreasoning
The observed pattern of pigmentation sweep timing was influenced by recent increases in European population size, which lowered drift and favored the accumulation of advantageous variants at different loci.
“We suggest that these patterns were influenced by recent increases in size of human populations, which favored the accumulation of advantageous variants at different loci.”
- Also stated in: § Introduction · hedged
“We suggest that this pattern was influenced by increases in European population size, which lowered the levels of drift and favored the recent accumulation of advantageous variants at different loci.”
Quote in the paperSubstantial claim - Also stated in: § Introduction · hedged
- Premisecitation
The well-known correlation between skin pigmentation and distance from the equator strongly suggests that natural selection in response to environmental factors played a major role in the geospatial patterning of human skin pigmentation variation.
“The well-known correlation between skin pigmentation and distance from the equator (Relethford 1997) strongly suggests that natural selection in response to environmental factors played a major role in the geospatial patterning of human skin pigmentation variation.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Relethford 1997 source
- Premisecitation
Derived alleles at SLC24A5, SLC45A2 and TYRP1 have a distribution primarily restricted to Europe.
“Other genes have derived alleles with a distribution primarily restricted to either Europe (SLC24A5, SLC45A2 and TYRP1) or East Asia (DCT and ATRN)”
Quote in the paperSubstantial claim0 of 3 sources checked - Study design and conductown data
In 98% of simulations, known parameter values fell within the range of the 95% HDR of the estimates.
“We found that in 98% of the simulations, the known parameter values fell within the range of the 95% HDR of the estimates.”
Quote in the paperSubstantial claim - Interpretationown data
The discrepancy for SLC45A2 is likely caused by recombinational introgression of microsatellite alleles with very different sizes into the background of the derived SLC45A2*G clade.
“This discrepancy is likely to have been caused by the recombinational introgression of microsatellite alleles with very different sizes into the background of the derived SLC45A2*G clade, as reflected in the bimodal allele frequency distributions at the microsatellite loci (TC)n and (TG)n3 (supplementary fig.S2, Supplementary Material online).”
Quote in the paperSubstantial claim - Interpretationreasoning
The more interspersed pattern at SLC45A2 is probably due to early recombination between ancestral and derived lineages.
“Haplotypes bearing the derived allele at the TYRP1 and SLC24A5 loci (fig.2A and B) tend to be more tightly clustered than at the SLC45A2 gene (fig.2C), which displays a more interspersed pattern, probably due to early recombination between ancestral and derived lineages.”
Quote in the paperNot a substantial claim - Interpretationown data
An important fraction of the KITLG*G intra-allelic variation was generated before the split of European and East Asian populations.
“suggesting that an important fraction of the KITLG*G intra-allelic vari- ation was generated before the split of European and East Asian populations (supplementary fig.S3, Supplementary Material online).”
Quote in the paperSubstantial claim - Interpretationcitation
The nonsignificant neutrality test values at KITLG likely reflect the limited power of the neutrality test to detect selective sweeps due to the added effects of recombination and high microsatellite mutation rates, which favor rapid recovery of intra-allelic variation.
“Thus, it is likely that the nonsignificant values may simply reflect the limited power of our neutrality test to detect selective sweeps due to the added effects of recombination and high microsatellite mutation rates, which favor the rapid recovery of intra-allelic variation (Wiehe 1998).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Wiehe 1998 source
- Interpretationreasoning
Lighter pigmentation alleles at SLC24A5, SLC45A2, and TYRP1 began to rise in frequency only in the latest phases of the Upper Paleolithic, encompassing the Solutrean and Magdalenian cultures.
“suggesting that lighter pigmentation alleles at these three loci began to rise in frequency only in the latest phases of the Upper Paleolithic, encompassing the Solutrean and the Magdalenian cultures.”
Quote in the paperSubstantial claim- Rests on an assumption: The four genes studied (KITLG, TYRP1, SLC24A5, SLC45A2) influence normal pigmentation variation.
- Premisenone given
Studies on admixed populations used a small number of ancestry informative markers to correct for admixture stratification.
“However, we note that these studies on admixed populations used a small number of ancestry informative markers to correct for admixture stratification.”
Quote in the paperSubstantial claim - Interpretationown data
The absence of signals of selection observed for the rs642742 locus may be a general feature of the KITLG gene when using this test.
“showing that that the absence of signals of selection we observe for the rs642742 locus may be a general feature of the KITLG gene when using this test.”
Quote in the paperSubstantial claim - Interpretationcitation
The substantially older estimates of sweep ages at KITLG than at SLC24A5, TYRP1, and SLC45A2 support the conclusion that the ability to detect selective sweeps with neutral microsatellites is inversely related with the time since fixation of a linked favorable allele.
“As the ability to detect selective sweeps with neutral microsatellites is inversely related with the time since fixation of a linked favorable allele (Wiehe 1998), this conclusion is also supported by the substantially older estimates of sweep ages at KITLG than at SLC24A5, TYRP1, and SLC45A (table 3), all three with significant neutrality tests (table 2).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Wiehe 1998 source
- Premisecitation
Archaeological data indicate a significant increase in population sizes in Europe at the Magdalenian (16,500-11,500 years ago).
“In support of this view are archeological data indicating that there was a significant increase in population sizes in Europe at the Magdalenian (16,500-11,500 years ago) (Bocquet-Appel and Demars 2000;Bocquet-Appel et al. 2005).”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
During the 11,000-19,000 years period over which selective sweeps at SLC24A5, SLC45A2, and TYRP1 started, effective population sizes could have been high enough for advantageous mutations to accumulate in relatively short time at different loci contributing to light pigmentation.
“On the contrary, during the 11,000-19,000 years period over which selective sweeps at SLC24A5, SLC45A2, and TYRP1 started, effective population sizes could have been high enough for advantageous mutations to accumulate in relatively short time at different loci contributing to light pigmentation.”
Quote in the paperSubstantial claim- Rests on an assumption: The four genes studied (KITLG, TYRP1, SLC24A5, SLC45A2) influence normal pigmentation variation.
- Premisecitation
Climatic conditions prevailing during the last glaciation likely favored cultural modifications that limited exposure to UVR, such as shelter seeking and wearing more protective clothing.
“As previously emphasized (Jablonski and Chaplin 2000), it is likely that the climatic conditions prevailing during the last glaciation favored cultural modifications that limited exposure to UVR, like shelter seeking and the wearing of more protective clothing.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Jablonski and Chaplin 2000 source
- May combine two claims. 18
- Classified as probably not a substantial claim. 11
- The quote only partly states this claim. 1
May combine two claims.
PremisecitationMost pigmentation genes have geospatial patterns of genetic variation correlated with the geographic distribution of skin pigmentation and display strong evidence for selective sweeps in European and East Asian populations.
“Most of these genes have geospatial patterns of genetic variation that are correlated with the geographic distribution of skin pigmentation and display strong evidence for selective sweeps in European and East Asian populations (Izagirre et al. 2006;McEvoy et al. 2006;Soejima et al. 2006;Voight et al. 2006;Lao et al. 2007;Myles et al. 2007;Norton et al. 2007;Sabeti et al. 2007;Williamson et al. 2”
Quote in the paperSubstantial claim2 of 3 sources checked- cites Izagirre et al. 2006 source
The EHH Test section reports significant selection signatures at only five of 32 tested loci after correction: three in Yorubans and two in Caucasians, with none in East Asians. The F ST Values section does report population-specific genetic differences at some loci, but it does not support the claim that most pigmentation genes show strong evidence of selective sweeps in European and East Asian populations. Page numbers are unavailable in our copy. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured - cites McEvoy et al. 2006 source
- cites Sabeti et al. 2007 source
The paper’s Abstract reports strong evidence of selection for two pigmentation genes, SLC24A5 and SLC45A2, in Europeans, and describes geographic differences in their variants. It does not establish the claim about most pigmentation genes or selective sweeps of pigmentation genes in East Asian populations; the Asian genes it highlights, EDAR and EDA2R, concern hair-follicle development. No page number is available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSeveral genes affecting melanin production and melanin function influence normal pigmentation variation in human populations.
“Recently, several genes affecting melanin production and melanin function have been shown to influence normal pigmentation variation in human populations by using association approaches and/or direct functional assays (reviewed in Parra 2007;Sturm 2009;Rees and Harding 2012).”
Quote in the paperNot a substantial claim1 of 3 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationKITLG derived alleles associated with lighter pigmentation reach high frequencies both in European and East Asian populations and likely began to be selected in a proto Eurasian population.
“Some genes, such as KITLG, have derived alleles (associated with lighter pigmentation) that reach high frequencies both in European and East Asian populations and likely began to be selected in a proto Eurasian population (Lao et al. 2007;Williamson et al. 2007;Pickrell et al. 2009).”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites Lao et al. 2007 source
- cites Williamson et al. 2007 source
The Results (page not specified) report strong evidence of selective sweeps near KITLG in both European-American and Chinese samples and suggest a role in human skin-pigmentation variation. They do not identify the selected alleles, establish that they are associated with lighter pigmentation or at high frequency in both populations, or place the start of selection in a proto-Eurasian population. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites Pickrell et al. 2009 source
The Pigmentation section (page unavailable) reports strong evidence of selection at KITLG in all non-African populations, and Novel selection candidates (page unavailable) links a nearby presumed selection target to skin pigmentation. Our copy does not establish that the lighter-pigmentation alleles are derived and at high frequency in both Europeans and East Asians, or that selection began in a proto-Eurasian population. (LLM, conf=0.84)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationSkin pigmentation has a complex evolutionary history, with selection acting on different genes at different times and geographic locations.
“In addition, the picture emerging from the genetic data suggests that skin pigmentation has a complex evolutionary history, with selection acting on different genes at different times and geographic locations (McEvoy et al. 2006;Lao et al. 2007;Myles et al. 2007;Norton et al. 2007;Pickrell et al. 2009).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites McEvoy et al. 2006 source
- cites Lao et al. 2007 source
- cites Pickrell et al. 2009 source
The Pigmentation section reports selection signals at several pigmentation genes that vary by region, and says light pigmentation in East Asia appears to have evolved largely through genes separate from those identified in European or African-American samples. It describes recent selection but does not establish that selection acted on different genes at different times. (LLM, conf=0.82)
Experimental — accuracy not yet measured
May combine two claims.
InterpretationcitationNonzero estimates for selection coefficients at KITLG contrast with nonsignificant values from neutrality tests but are consistent with scans for selection based on SNPs.
“The nonzero estimates for selection coefficients at KITLG (table 3) contrast with the nonsignificant values obtained with our neutrality tests (table 2) but are consistent with scans for selection based on SNPs (McEvoy et al. 2006;Lao et al. 2007;Miller et al. 2007;Williamson et al. 2007;Pickrell et al. 2009).”
Quote in the paperSubstantial claim1 of 3 sources checkedClassified as probably not a substantial claim.
PremisecitationHuman populations migrating to higher latitudes moved from a darkly pigmented ancestral state toward lighter pigmentation due to genetic adaptation in response to spatially varying selective pressures.
“Taken together, these findings are broadly consistent in showing that human populations migrating to higher latitudes moved from a darkly pigmented ancestral state toward lighter pigmentation due to genetic adaptation in response to spatially varying selective pressures (Jablonski and Chaplin 2000;Jablonski 2004;Parra 2007).”
Quote in the paperSubstantial claim1 of 3 sources checkedClassified as probably not a substantial claim.
PremisecitationThe geographic spread of selected variants essentially depends on the timing of selective sweeps relative to major population movements.
“Recently, it has been suggested that the geographic spread of selected variants essentially depends on the timing of selective sweeps relative to major population movements (Coop et al. 2009).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Coop et al. 2009 source
May combine two claims. The quote only partly states this claim.
Interpretationown dataThe initial stages of European skin lightening occurred in a proto-Eurasian population approximately 30,000 years ago, after the out-of-Africa migration 60,000-70,000 years ago and slightly more recently than the earliest archaeological evidence for anatomically modern humans in Europe approximately 40,000 years ago.
“Our results based on the KITLG gene suggest that the initial stages of European skin lightening occurred in a proto-Eurasian population, approximately 30,000 years ago”
Quote in the paperSubstantial claim1 of 3 sources checked- cites Schaffner et al. 2005 source
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured - cites Mellars 2006 source
- cites Keinan et al. 2007 source
- Rests on an assumption: The four genes studied (KITLG, TYRP1, SLC24A5, SLC45A2) influence normal pigmentation variation.
May combine two claims.
PremisecitationRecent estimates based on genome-wide patterns of variation suggest that European and East Asian divergence might have occurred as late as 25,000 years ago, implying that colonization of Europe could have involved several migration movements at different ages.
“Recent estimates based on genome-wide patterns of variation have suggested that the European and East Asian divergence might have occurred as late as 25,000 years ago (Keinan et al. 2007;Gutenkunst et al. 2009;Laval et al. 2010;Rasmussen et al. 2011), implying that the colonization of Europe could have involved several migration movements at different ages (Laval et al. 2010).”
Quote in the paperSubstantial claim2 of 3 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
FindingcitationTag SNP allele frequencies in the samples mirrored previously described distributions in major geographic groups.
“As expected, the tag SNP allele frequencies in our samples mirrored previously described distributions in major geographic groups (Lamason et al. 2005;Yuasa et al. 2006;Frazer et al. 2007;Miller et al. 2007;Norton et al. 2007;Soejima and Koda 2007) (table 1).”
Quote in the paperNot a substantial claim1 of 3 sources checkedMay combine two claims.
PremisecitationThe demographic model most compatible with the data for European and East Asian populations is a bottleneck scenario, with stronger genetic drift in East Asian populations than European populations.
“Recent studies have shown that the demographic model most compatible with the data for European and East Asian populations is a bottleneck scenario, with stronger genetic drift in East Asian populations than European populations (Schaffner et al. 2005;Voight et al. 2005).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites Schaffner et al. 2005 source
The Discussion’s Table 1 gives the best-fitting simulation a stronger Asian bottleneck (F = 0.067) than European bottleneck (F = 0.020), consistent with greater drift in the Asian lineage. But the Discussion says many other models could fit acceptably and cautions that its parameters are not inferences about real-world history. It therefore does not establish a bottleneck scenario as the uniquely most compatible demographic history. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites Voight et al. 2005 source
The Discussion concludes that simple bottleneck models can explain the non-African data. In “Testing Bottleneck Models in the Non-African Data” (page unavailable), the Chinese sample admits slightly more severe bottlenecks than the Italian sample under a 40,000-year onset, but the compatible ranges are similar and milder Chinese bottlenecks cannot be rejected under an 80,000-year onset. The paper therefore does not establish stronger genetic drift in East Asians as an unqualified finding, or identify a single most-compatible model. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim. May combine two claims.
PremisecitationRecent theoretical work has shown that independent evolution may be an important determinant of geographic patterns of adaptation and could explain the observed scarcity of continental-wide sweeps in human populations, even when selective pressures are homogeneous.
“Recent theoretical work (Ralph and Coop 2010) has shown that independent evolution may be an important determinant of geographic patterns of adaptation and could explain the observed scarcity of continental-wide sweeps in human populations (Coop et al. 2009;Pickrell et al. 2009), even when selective pressures are homogeneous.”
Quote in the paperSubstantial claim3 of 3 sources checked- cites Ralph and Coop 2010 source
- cites Coop et al. 2009 source
- cites Pickrell et al. 2009 source
The Assessment of power section reports limited sharing of selection signals between some geographic regions, supporting the observation that many signals are geographically restricted. It also reports extensive sharing within geographic regions, so it does not clearly establish a scarcity of sweeps spanning an entire continent. The theoretical explanation is attributed to Ralph and Coop (2010), not to this paper. (LLM, conf=0.76)
Experimental — accuracy not yet measured
May combine two claims.
FindingcitationThe derived alleles SLC24A5*A and SLC45A2*G both have frequencies higher than 90% in Europeans but are much more rare or absent in Africans and East Asians.
“The derived alleles SLC24A5*A and SLC45A2*G both have frequencies higher than 90% in Europeans but are much more rare or absent in Africans and East Asians.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe TYRP1*G allele is rare among Africans and East Asians and reaches an intermediate frequency of 60% in Europeans.
“The TYRP1*G allele, which is also rare among Africans and East Asians, reaches an intermediate frequency of 60% in Europeans.”
Quote in the paperNot a substantial claimMay combine two claims.
FindingcitationModified demographic conditions did not strongly affect the simulation results; t and s varied on average approximately 18% and 4% of estimates assuming constant population size under the dominant and additive models, respectively.
“the modified demographic conditions did not strongly affect the simulation results, with t and s varying on average approximately 18% and 4% of the size of estimates obtained assuming constant population size, under the dominant and the additive models, respectively.”
Quote in the paperSubstantial claim0 of 3 sources checkedMay combine two claims.
FindingreasoningOur estimates for the onset of selection at KITLG are consistent with these findings, although more ancient dates (>40,000 years) cannot be excluded due to uncertainty of age estimates.
“Our estimates for the onset of selection at KITLG are consistent with these findings, although more ancient dates (>40,000 years) cannot be excluded, due to uncertainty of age estimates.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe onset of selective sweeps at SLC24A5, SLC45A2, and TYRP1 was much more recent than at KITLG and remarkably compressed within the last 11,000-19,000 years.
“Our estimates additionally show that the onset of selective sweeps at SLC24A5, SLC45A2, and TYRP1, the three genes in which the geographic distribution of the polymorphisms is primarily restricted to European populations, was much more recent than at KITLG and remarkably compressed within the last 11,000-19,000 years (table 3)”
Quote in the paperSubstantial claim0 of 1 sources checked- cites table 3
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Rests on an assumption: The four genes studied (KITLG, TYRP1, SLC24A5, SLC45A2) influence normal pigmentation variation.
May combine two claims.
Findingown dataOur sweep age estimates for KITLG, SLC24A5, SLC45A2, and TYRP1 are consistent with the interpretation that the onset of the Eurasian-wide sweep at KITLG precedes the split of Europeans and East Asians, whereas the European-specific sweeps at SLC24A5, SLC45A2, and TYRP1 started well after the separation of European populations.
“Our sweep age estimates for KITLG, SLC24A5, SLC45A2, and TYRP1 are consistent with this interpretation, because the onset of the Eurasian-wide sweep at KITLG precedes the split of Europeans and East Asians, whereas the European-specific sweeps at SLC24A5, SLC45A2, and TYRP1 started well after the separation of European populations.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Premisenone givenSeveral candidate genes for skin pigmentation exhibit patterns of polymorphism that overlap the geospatial variation in skin color.
“Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S1 (asserted).
PremisecitationSelection favored lighter skin to maximize the production of vitamin D in regions with lower UVR.
“it has been suggested that selection favored lighter skin to maximize the production of vitamin D in regions with lower UVR (Loomis 1967;Jablonski and Chaplin 2000).”
Quote in the paperNot a substantial claim0 of 2 sources checkedClassified as probably not a substantial claim.
PremisecitationThe inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin to facilitate vitamin D synthesis in regions far from the equator.
“The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin to facilitate vitamin D synthesis in regions far from the equator.”
Quote in the paperSubstantial claim0 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationOne prior study suggested that the selective sweep at SLC45A2 occurred long after the arrival of anatomically modern humans in Europe.
“One prior study has similarly suggested that the selective sweep at the SLC45A2 occurred long after the arrival of anatomically modern humans in Europe (Soejima et al. 2006).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Soejima et al. 2006 source
May combine two claims.
InterpretationreasoningAlthough the direction of strength of the alleles might be correct, the size of the effect of the genes could be overestimated.
“Hence, although the direction of strength of the alleles might be correct, the size of the effect of the genes could be overestimated.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationown dataBoth the modal age estimates and the extensive sharing of derived lineages between European and East Asian populations suggest that the onset of the KITLG sweep occurred before the divergence of the ancestors of present-day Europeans and East Asians, well after modern humans left Africa.
“In any case, both the modal age estimates (table 3) and the extensive sharing of derived lineages between European and East Asian populations (supplementary fig.S3, Supplementary Material online) suggest that the onset of the KITLG sweep occurred before the divergence of the ancestors of present-day Europeans and East Asians, well after modern humans left Africa.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
PremisecitationThe rate of adaptive evolution in humans before 50,000 years was relatively low, starting to increase only with the onset of population growth in the Upper Paleolithic and its subsequent magnification during the Neolithic.
“Because of this limiting effect, it has been proposed that the rate of adaptive evolution in humans before 50,000 years was relatively low, starting to increase only with the onset of population growth in the Upper Paleolithic and its subsequent magnification during the Neolithic (Hawks et al. 2007).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Hawks et al. 2007 source
May combine two claims.
InterpretationcitationThe temporal patterns reported here for pigmentation lightening are likely far from unique and may be exhibited by a substantial proportion of other recently evolved traits.
“In this framework, the temporal patterns reported here for pigmentation lightening are likely to be far from unique and may be exhibited by a substantial proportion of other recently evolved traits.”
Quote in the paperNot a substantial claim- Rests on an assumption: The four genes studied (KITLG, TYRP1, SLC24A5, SLC45A2) influence normal pigmentation variation.
May combine two claims.
PremisecitationThe period encompassing the onset of the SLC24A5, SLC45A2, and TYRP1 sweeps (11,000-19,000 years ago) falls within oxygen-isotope climatic stage 2 (OIS-2), which lasted from 24,000 to 12,000 years ago and comprised the last glacial maximum approximately 15,000-20,000 years ago.
“The period encompassing the onset of the SLC24A5, SLC45A2, and TYRP1 sweeps, between 11,000 and 19,000 years ago, falls within the oxygen-isotope climatic stage 2 (OIS-2), which lasted from 24,000 to 12,000 years ago and comprised the last glacial maximum (LGM), approximately 15,000-20,000 years ago (Klein 1999).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Klein 1999
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
The paper relies on this without support.
Little work has focused on estimating the time frame over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes.
“However, little work has focused on estimating the time frame over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes.”
“However, limited work has focused on estimating the time frame over which pigmentation changed and on the intensity of selection acting upon different genes.”
The authors state this as an assumption.
The haplotype combining the modal allele at each microsatellite locus represents the original haplotype.
“To calculate P anc values from the data, we assumed that the haplotype combining the modal allele at each microsatellite locus represented the original haplotype (Coelho et al. 2005).”
The authors state this as an assumption.
Reverse mutation in microsatellites is negligible.
“We did not consider the regeneration of the original haplotype due to reverse mutation in microsatellites, because it is expected to be negligible given the relatively high number of microsatellite loci used to define haplotypes.”
The authors state this as an assumption.
Fitness effects are additive or fully dominant.
“All estimates are based on 10,000 accepted simulations and assume an additive or fully dominant fitness effect.”
The paper relies on this without support.
The four genes studied (KITLG, TYRP1, SLC24A5, SLC45A2) influence normal pigmentation variation.
“four genes influencing normal pigmentation variation”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
An attempt to date the origin of the SLC24A5 allele yielded a 95% confidence interval of 6,000 to 38,000 years ago, overlapping with the time interval when TCC to T rate seems to have accelerated.
“An attempt to date the origin of this allele yielded a 95% confidence interval of 6,000-38,000 y ago (26), which overlaps with the time interval when the TCC → T rate seems to have accelerated.”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [26]
Three pigmentation SNPs display European-specific selective sweeps presumed to facilitate vitamin D synthesis and estimated as having occurred within the last 11,000-19,000 years.
“In particular we examined three pigmentation SNPs that display European-specific selective sweeps that are presumed to facilitate vitamin D synthesis and estimated as having occurred within the last 11,000–19,000 years33.”
From Genome flux and stasis in a five millennium transect of European prehistory (2014) · cites this paper as [33]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
The target-gene list names a different gene
MinorThe introduction lists SLC25A5 among the four genes analyzed, whereas the methods and results identify that gene as SLC24A5.
“KITLG, SLC25A5, and SLC45A2, which explain a significant portion of the skin color differences between European and West African populations”
“Tag SNPs at SLC24A5 (rs1426654G>A), SLC45A2 (rs16891982C>G), KITLG (rs642742A>G) and TYRP1 (rs2733831A>G) loci were chosen”
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Soejima, M., & Koda, Y. (2006) · International Journal of Legal Medicine · doi:10.1007/s00414-006-0112-z · Cited by 128 · see citing works
Edwards, M., Bigham, A., Tan, J., Li, S., Gozdzik, A., Ross, K., Jin, L., & Parra, E. J. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000867 · Cited by 128 · see citing works
Self-citationPopulation kinetics in the Upper Palaeolithic in Western Europe
Bocquet-Appel, J.-P., & Demars, P.-Y. (2000) · Journal of Archaeological Science · doi:10.1006/jasc.1999.0471 · Cited by 126 · see citing works
Recombination rates in admixed individuals identified by ancestry-based inference
Wegmann, D., Kessner, D., Veeramah, K., Mathias, R., Nicolae, D., Yanek, L., Sun, Y. V., Torgerson, D., Rafaels, N., Mosley, T., et al. (2011) · Nature Genetics · doi:10.1038/ng.894 · Cited by 119 · see citing works
A scan for signatures of positive selection in candidate loci for skin pigmentation in humans
Izagirre, N., García, I., Junquera, C., de la Rúa, C., & Alonso, S. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl030 · Cited by 119 · see citing works
Microsatellite variation and evolution of human lactase persistence
Coelho, M., Luiselli, D., Bertorelle, G., Lopes, A. I., Seixas, S., Destro‐Bisol, G., & Rocha, J. (2005) · Human Genetics · doi:10.1007/s00439-005-1322-z · Cited by 118 · see citing works
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Evidence for recent positive selection at the human AIM1 locus in a European population
Soejima, M., Tachida, H., Ishida, T., Sano, A., & Koda, Y. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msj018 · Cited by 84 · see citing works
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The human career human biological and cultural origins
Klein, R. G. (2009) · Cited by 75 · see citing works
Faunal extinction in an island society: Pygmy hippopotamus hunters of Cyprus
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Estimating Effective Population Size or Mutation Rate With Microsatellites
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Understanding the evolution of human pigmentation: recent contributions from population genetics
Rees, J. L., & Harding, R. M. (2012) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.358 · Cited by 50 · see citing works
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Mutation Rate Variation at Human Dinucleotide Microsatellites
Xu, H., Chakraborty, R., & Fu, Y. (2005) · Genetics · doi:10.1534/genetics.104.036855 · Cited by 23 · see citing works
Hemispheric difference in human skin color
Relethford, J. H. (1997) · American Journal of Physical Anthropology · doi:10.1002/(sici)1096-8644(199712)104:4
Hemispheric difference in human skin color
Chaplin, G., & Jablonski, N. G. (1998) · American Journal of Physical Anthropology · doi:10.1002/(sici)1096-8644(199810)107:2
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- Gamble, 1990, Pleistocene polyphony: the diversity of human adaptations at the last glacial maximum
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Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
Haber, M., Mezzavilla, M., Xue, Y., & Tyler-Smith, C. (2016) · Genome Biology · doi:10.1186/s13059-015-0866-z · Cited by 1,924 · see citing works
“It was thought that the light skin of Europeans was a Paleolithic adaptation to facilitate vitamin D production in reduced sunlight regions [43].”
BackgroundAncient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
Genome flux and stasis in a five millennium transect of European prehistory
Gamba, C., Jones, E. R., Teasdale, M. D., McLaughlin, R. L., Gonzalez-Fortes, G., Mattiangeli, V., Domboróczki, L., Kővári, I., Pap, I., Anders, A., et al. (2014) · Nature Communications · doi:10.1038/ncomms6257 · Cited by 667 · see citing works
“In particular we examined three pigmentation SNPs that display European-specific selective sweeps that are presumed to facilitate vitamin D synthesis and estimated as having occurred within the last 11,000–19,000 years 33 .”
Detection of human adaptation during the past 2000 years
Field, Y., Boyle, E. A., Telis, N., Gao, Z., Gaulton, K. J., Golan, D., Yengo, L., Rocheleau, G., Froguel, P., McCarthy, M. I., et al. (2016) · Science · doi:10.1126/science.aag0776 · Cited by 383 · see citing works
Loci associated with skin pigmentation identified in African populations
Crawford, N. G., Kelly, D., Hansen, M. E. B., Beltrame, M., Fan, S.-H., Bowman, S. L., Jewett, E., Ranciaro, A., Thompson, S., Lo, Y., et al. (2017) · Science · doi:10.1126/science.aan8433 · Cited by 345 · see citing works
“On the basis of coalescent analysis with sequence data from the Simons Genomic Diversity Project (SGDP) (13), the time tomost recent common ancestor (TMRCA) ofmost Eurasian lineages containing the rs1426654 (A) allele is 29 thousand years ago (ka) [95% critical interval (CI), 28 to 31 ka], consistent with previous stu…”
Wilde, S., Timpson, A., Kirsanow, K., Kaiser, E., Kayser, M., Unterländer, M., Hollfelder, N., Potekhina, I. D., Schier, W., Thomas, M. G., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1316513111 · Cited by 257 · see citing works
“Signatures of recent natural selection have been detected in some pigmentation genes, including both shared and regionally specific alleles associated with lighter skin pigmentation in eastern and western Eurasia (13, 14), using modern population genetic data (1, 12,”
BackgroundMethodInfluentialOlalde, I., Schroeder, H., Sandoval-Velasco, M., Vinner, L., Lobón, I., Ramirez, O., Civit, S., García Borja, P., Salazar-García, D. C., Talamo, S., et al. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv181 · Cited by 207 · see citing works
“screen for phenotypic traits of interest that have been the subject of recent natural selection in Europeans, according to several studies (Beleza et al. 2013; Grossman et al. 2013).”
ResultHuman pigmentation genes under environmental selection
Sturm, R. A., & Duffy, D. L. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-248 · Cited by 203 · see citing works
Harnessing ancient genomes to study the history of human adaptation
Marciniak, S., & Perry, G. H. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.65 · Cited by 182 · see citing works
A genomic perspective on HLA evolution
Meyer, D., Aguiar, V. R. C., Bitarello, B. D., Brandt, D. Y. C., & Nunes, K. (2017) · Immunogenetics · doi:10.1007/s00251-017-1017-3 · Cited by 182 · see citing works
“In some cases, it is possible to provide mechanistic links between the favored variant and its phenotypic effect, and to estimate the timescale of selection (for example, in the cases of variants involved in pigmentation (Beleza et al. 2013), lactase persistence (Coelho et al.”
BackgroundVitamin D: calcium and bone homeostasis during evolution.
Bouillon, R., & Suda, T. (2014) · BoneKEy Reports · doi:10.1038/bonekey.2013.214 · Cited by 184 · see citing works
Evidence for recent, population-specific evolution of the human mutation rate
Harris, K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418652112 · Cited by 165 · see citing works
“An attempt to date the origin of this allele yielded a 95% confidence interval of 6,000–38,000 y ago (26), which overlaps with the time interval when the TCC→T rate seems to have accelerated.”
BackgroundAn Unexpectedly Complex Architecture for Skin Pigmentation in Africans
Martin, A. R., Lin, M., Granka, J. M., Myrick, J. W., Liu, X., Sockell, A., Atkinson, E. G., Werely, C. J., Möller, M., Sandhu, M. S., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.015 · Cited by 156 · see citing works
The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent
Mallick, C. B., Iliescu, F. M., Möls, M., Hill, S. C., Tamang, R., Chaubey, G., Goto, R., Ho, S. Y. W., Romero, I. G., Crivellaro, F., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003912 · Cited by 120 · see citing works
“Besides this, a recent study by Beleza [42], focusing on analyses of diversity in microsatellite loci, estimated that the selective sweep at SLC24A5 occurred around 11.3 KYA (95% CI, 1–55.8 KYA) and 18.7 KYA (5.8–38.3 KYA) under additive and dominant models, respectively [42].”
BackgroundResultInfluentialAdaptation of human skin color in various populations
Deng, L., & Xu, S. (2017) · Hereditas · doi:10.1186/s41065-017-0036-2 · Cited by 112 · see citing works
Understanding rare and common diseases in the context of human evolution
Quintana‐Murci, L. (2016) · Genome biology · doi:10.1186/s13059-016-1093-y · Cited by 97 · see citing works
“The large number of studies searching for selection signals contrasts with the much smaller number of studies trying to determine when selection effects occurred [83, 129, 130].”
ResultVitamin D and evolution: Pharmacologic implications
Hänel, A., & Carlberg, C. (2019) · Biochemical Pharmacology · doi:10.1016/j.bcp.2019.07.024 · Cited by 111 · see citing works
Harris, A. M., Garud, N. R., & DeGiorgio, M. (2018) · Genetics · doi:10.1534/genetics.118.301502 · Cited by 83 · see citing works
“[Przeworski et al., 2005, Berg and Coop, 2015].”
Population genomics of human adaptation
Lachance, J., & Tishkoff, S. A. (2013) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-110512-135833 · Cited by 95 · see citing works
“SIFT classifies mutations as “tolerated” or “damaging” (Fu 1997), and PolyPhen-2 classifies mutations as “benign”, “possibly damaging”, or “probably damaging” (Beleza et al 2013).”
Range Expansion Compromises Adaptive Evolution in an Outcrossing Plant
González‐Martínez, S. C., Ridout, K. E., & Pannell, J. R. (2017) · Current Biology · doi:10.1016/j.cub.2017.07.007 · Cited by 85 · see citing works
Teruel, B. M., Parra, E. J., Fuentes-Smith, E., Salas, A., Buttenschøn, H. N., Demontis, D., Torres, M. L., Padrón, L. C. M., Gómez-Cabezas, E. J., Álvarez‐Iglesias, V., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004488 · Cited by 93 · see citing works
“These polymorphisms have been associated with pigmentary phenotypes in previous studies [21–37].”
BackgroundMethodResultSelf-citationJablonski, N. G. (2021) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12976 · Cited by 93 · see citing works
Searching for Sympatric Speciation in the Genomic Era
Richards, E. J., Servedio, M. R., & Martin, C. H. (2019) · BioEssays · doi:10.1002/bies.201900047 · Cited by 85 · see citing works
Adaptations to local environments in modern human populations
Jeong, C., & Di Rienzo, A. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.06.011 · Cited by 80 · see citing works
Timmermann, A. (2020) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2020.106331 · Cited by 84 · see citing works
Colorful DNA polymorphisms in humans
Liu, F., Wen, B., & Kayser, M. (2013) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2013.03.013 · Cited by 81 · see citing works
Estimating Time to the Common Ancestor for a Beneficial Allele
Smith, J., Coop, G., Stephens, M., & Novembre, J. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy006 · Cited by 66 · see citing works
“…which shows significant effects on skin pigmentation differences between Europeans and Africans [Miller et al., 2007]; although more recent work fails to find any contribution of KITLG toward variation in skin pigmentation in a Cape Verde African-European admixed population [Beleza et al., 2013a].”
BackgroundResultInfluentialSkin colour and vitamin D: An update
Hänel, A., & Carlberg, C. (2020) · Experimental Dermatology · doi:10.1111/exd.14142 · Cited by 76 · see citing works
Shades of complexity: New perspectives on the evolution and genetic architecture of human skin
Quillen, E. E., Norton, H. L., Parra, E. J., Lona‐Durazo, F., Ang, K. C., Illiescu, F. M., Pearson, L. N., Shriver, M. D., Lasisi, T., Gokcumen, O., et al. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23737 · Cited by 67 · see citing works
“Studies of genomes from remains dating up to 8,000 years ago reveal that most present-day Europeans derive ancestry from west European hunter-gatherers, among whom the derived OCA2/HERC2 allele was already at high frequency, as well as early farmers from Anatolia and northern Eurasians, among whom the derived allele f…”
BackgroundInfluentialSelf-citationPinto, J. C., Oliveira, S., Teixeira, S., Martins, D., Fehn, A., Aço, T., Gayà‐Vidal, M., & Rocha, J. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23042 · Cited by 61 · see citing works
Self-citationAnthropological perspectives on genomic data, genetic ancestry, and race
Torres, J. B. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23979 · Cited by 63 · see citing works
Association of Genetic Variants with Self-Assessed Color Categories in Brazilians
Durso, D. F., Bydlowski, S. P., Hutz, M. H., Suarez‐Kurtz, G., Magalhães, T. R., & Pena, S. D. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0083926 · Cited by 61 · see citing works
“The difference was that SNP rs642742 close to gene KITLG now was also significant, while it had not been significant with the Rio de Janeiro sample.”
Hider, J., Gittelman, R. M., Shah, T., Edwards, M., Rosenbloom, A., Akey, J. M., & Parra, E. J. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-150 · Cited by 55 · see citing works
“These findings support an evolutionary model in which the most important changes in pigmentary traits occurred after the migration out-of-Africa and the separation of the lineages that gave rise to contemporary European and East Asian populations [5,12,22-25].”
ResultSelf-citationThe African diaspora: history, adaptation and health
Rotimi, C. N., Ayele, F. T., Baker, J. L., & Shriner, D. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.08.005 · Cited by 55 · see citing works
A hidden Markov model for investigating recent positive selection through haplotype structure
Chen, H., Hey, J., & Slatkin, M. (2014) · Theoretical Population Biology · doi:10.1016/j.tpb.2014.11.001 · Cited by 56 · see citing works
The Evolutionary History of Human Skin Pigmentation
Rocha, J. (2019) · Journal of Molecular Evolution · doi:10.1007/s00239-019-09902-7 · Cited by 50 · see citing works
Self-citationYang, Z., Shi, H., Ma, P., Zhao, S., Kong, Q., Bian, T., Gong, C., Zhao, Q., Liu, Y., Qi, X., et al. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy136 · Cited by 42 · see citing works
Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin
Kita, R., & Fraser, H. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006382 · Cited by 22 · see citing works
Estimating the Ages of Selection Signals from Different Epochs in Human History
Nakagome, S., Alkorta‐Aranburu, G., Amato, R., Howie, B., Peter, B. M., Hudson, R. R., & Rienzo, A. D. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv256 · Cited by 38 · see citing works
“The ages of skin pigmentation alleles have been previously estimated based on microsatellite (Beleza et al. 2013) and sequence variation (Soejima et al. 2006) data.”
BackgroundMethodResultInfluentialKalantzis, M., & Cope, B. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108862059 · Cited by 62 · see citing works
Engelken, J., Carnero‐Montoro, E., Pybus, M., Andrews, G. K., Lalueza‐Fox, C., Comas, D., Sekler, I., Vives, M. D. L. R., Rosas, A., Stoneking, M., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004128 · Cited by 39 · see citing works
“[40]).”
Geographical ancestry is a key determinant of epidermal morphology and dermal composition
Langton, A. K., Sherratt, M. J., Sellers, W. I., Griffiths, C. E. M., & Watson, R. E. B. (2014) · British Journal of Dermatology · doi:10.1111/bjd.12860 · Cited by 40 · see citing works
Living in an adaptive world: Genomic dissection of the genus Homo and its immune response
Quach, H., & Quintana‐Murci, L. (2017) · The Journal of Experimental Medicine · doi:10.1084/jem.20161942 · Cited by 39 · see citing works
“…2009); genes involved in the variation of skin pigmentation and hair morphology (Lamason et al., 2005; Miller et al., 2007; Norton et al., 2007; Beleza et al., 2013); genes involved in adaptation to diverse habitats, from the rainforest to hypoxic conditions at high altitude (Bigham et al.,…”
BackgroundInfluentialImplications of the Admixture Process in Skin Color Molecular Assessment
de Cerqueira, C. C. S., Hünemeier, T., Gómez‐Valdés, J., Ramallo, V., Krause, C. D. D. V., Barbosa, A. A. L., Vargas‐Pinilla, P., Dornelles, R. C., Longo, D., Rothhammer, F., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096886 · Cited by 39 · see citing works
“Furthermore, it has been suggested that some variants associated with pigmentation also confer susceptibility or resistance to skin cancer [12,20,21], since the presence of various skin tones is attributed to adaptation to diverse environments after dispersal of the anatomically modern Homo sapiens from Africa to othe…”
BackgroundEaton, K., Edwards, M., Krithika, S., Cook, G. R., Norton, H., & Parra, E. J. (2015) · American Journal of Human Biology · doi:10.1002/ajhb.22678 · Cited by 36 · see citing works
“The derived alleles of rs1426654 (allele A) and rs16891982 (allele G) have reached extremely high frequencies in some European populations through a recent selective sweep (Beleza et al., 2013; Norton et al., 2007) but are absent or present at very low frequencies in African and East Asian populations (Norton et al.”
BackgroundSelf-citationLucock, M. D. (2022) · American Journal of Biological Anthropology · doi:10.1002/ajpa.24564 · Cited by 35 · see citing works
“Even more relevant, selective sweeps for Europeanspecific alleles in three genes—TYRP1, SLC24A5, and SLC45A2 occurred far later, within the last 11,000–19,000 years, long after the first dispersals of modern humans into Europe (Beleza et al., 2013).”
BackgroundInferring evolutionary dynamics of mutation rates through the lens of mutation spectrum variation
Carlson, J., DeWitt, W. S., & Harris, K. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.024 · Cited by 24 · see citing works
“During the late Pleistocene (between 11–19kya), human populations in Europe also acquired adaptive mutations in multiple genes that conferred lighter skin pigmentation, which rapidly swept to high frequency throughout most of Europe [70].”
BackgroundDrivers of plateau adaptability in cashmere goats revealed by genomic and transcriptomic analyses
Wu, C., Ma, S., Zhao, B., Qin, C., Wu, Y., Di, J., Suo, L., & Fu, X. (2023) · BMC Genomics · doi:10.1186/s12864-023-09333-1 · Cited by 33 · see citing works
“MITF and KITLG genes play a crucial role in the melanin biosynthesis and pigmentation [17, 18].”
BackgroundEvolutionary genetics of skin pigmentation in African populations
Feng, Y., McQuillan, M. A., & Tishkoff, S. A. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab007 · Cited by 31 · see citing works
“A derived, nonsynonymous mutation (rs1426654 (A), Ala111Thr) in SLC24A5 associated with light skin color has swept to near fixation in Europeans due to positive selection (13,22,70,71).”
BackgroundRawofi, L., Edwards, M., Krithika, S., Le, P., Cha, D., Yang, Z., Ma, Y., Wang, J., Su, B., Li, J., et al. (2017) · PeerJ · doi:10.7717/peerj.3951 · Cited by 31 · see citing works
“…technologies, which have made it possible to 50 obtain quantitative measurements of skin, hair and iris pigmentation (Liu et al., 2010; Walsh et 51 al., 2011; Edwards et al., 2012; Beleza et al., 2013; Andersen et al., 2013; Norton et al., 2015; 52 Edwards et al., 2015; Wollstein et al., 2017).”
BackgroundResultInfluentialSelf-citationMoore, C., Wallace, J. R., Wolfe, D., Frase, A., Pendergrass, S. A., Weiss, K. M., & Ritchie, M. D. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003959 · Cited by 31 · see citing works
“European specific selective sweeps estimated in the last 20,000 years suggest that SLC24A5 is key in skin pigmentation and Zebrafish with ‘‘golden’’ mutations exhibit melanosomal changes [28–30].”
BackgroundGlobal Patterns of Diversity and Selection in Human Tyrosinase Gene
Hudjashov, G., Villems, R., & Kivisild, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074307 · Cited by 31 · see citing works
“Overall, the most recent common ancestors of both haplogroups appear to, at least partly, overlap with the time period at which the selective sweeps at three other pigmentation genes, SLC24A5, SLC45A2 and TYRP1, have been estimated [23,99].”
BackgroundA Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years
Zhou, H., Hu, S., Matveev, R., Yu, Q., Li, J., Khaitovich, P., Jin, L., Lachmann, M., Stoneking, M., Fu, Q., et al. (2015) · doi:10.1101/018929 · Cited by 28 · see citing works
Norton, H. L., Edwards, M., Krithika, S., Johnson, M., Werren, E. A., & Parra, E. J. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22861 · Cited by 30 · see citing works
Self-citationLatitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes
Tiosano, D., Audı́, L., Climer, S., Zhang, W., Templeton, A. R., Fernández‐Cancio, M., Gershoni‐Baruch, R., Sánchez-Muro, J. M., Kholy, M. E., & Hochberg, Z. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.026773 · Cited by 27 · see citing works
Elias, P. M., & Williams, M. L. K. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23030 · Cited by 28 · see citing works
“The recent revelation that epidermal pigmentation remained quite dark in central European Mesolithic humans (Beleza et al., 2013; Olalde et al., 2014; Wilde et al., 2014), led to a modification of the VD3 hypothesis, based upon the putative dietary inadequacies of cerealbased diets in later, agrarian societies (Khan &…”
BackgroundLópez, S., Garcı́a, O., Yurrebaso, I., Flores, C., Acosta‐Herrera, M., Chen, H., Gardeazábal, J., Careaga, J. M., Boyano, M. D., Sánchez, A., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0104367 · Cited by 25 · see citing works
“These estimations support the work by Beleza et al. [42], who reported that the age of the allele ranged between 8,260–31,780 years under a dominant model and between 6,188– 26,964 years under an additive model, after the arrival of modern humans in Europe, and similarly to other light pigmentation alleles such as all…”
BackgroundMolecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection
Canfield, V. A., Berg, A. S., Peckins, S., Wentzel, S. M., Ang, K. C., Oppenheimer, S., & Cheng, K. C. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.007484 · Cited by 29 · see citing works
Jonnalagadda, M., Norton, H., Ozarkar, S., Kulkarni, S. S., & Ashma, R. (2016) · American Journal of Human Biology · doi:10.1002/ajhb.22836 · Cited by 22 · see citing works
Novel genomic signals of recent selection in an Ethiopian population
Ayele, F. T., Adeyemo, A., Chen, G., Hailu, E., Aseffa, A., Davey, G., Newport, M. J., & Rotimi, C. N. (2014) · European Journal of Human Genetics · doi:10.1038/ejhg.2014.233 · Cited by 25 · see citing works
Sun Exposure, Sunbeds and Sunscreens and Melanoma. What Are the Controversies?
Bataille, V. A. (2013) · Current Oncology Reports · doi:10.1007/s11912-013-0342-4 · Cited by 27 · see citing works
Uncovering Footprints of Natural Selection Through Spectral Analysis of Genomic Summary Statistics
Arnab, S. P., Amin, M. R., & DeGiorgio, M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad157 · Cited by 18 · see citing works
“Application of SISSSCO to European human genome variation gave high support for previously identified sweeps at the LCT , ABCA12 , and SLC45A2 genes (Bersaglieri et al. 2004; Beleza et al. 2013; Sirica et al. 2019), as well as 19 other candidate genes with high confidence.”
How well do we understand the basis of classic selective sweeps in humans?
Szpak, M., Xue, Y., Ayub, Q., & Tyler‐Smith, C. (2019) · FEBS Letters · doi:10.1002/1873-3468.13447 · Cited by 23 · see citing works
Rapid evolution of a skin-lightening allele in southern African KhoeSan
Lin, M. H., Siford, R. L., Martin, A. R., Nakagome, S., Möller, M., Hoal, E. G., Bustamante, C. D., Gignoux, C. R., & Henn, B. M. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1801948115 · Cited by 24 · see citing works
“(21) ABC (microsatellites) Europeans 11 [1 to 55] Nakagome et al.”
BackgroundThe Puzzle of European Hair, Eye, and Skin Color
Fröst, P. (2014) · Advances in Anthropology · doi:10.4236/aa.2014.42011 · Cited by 25 · see citing works
“European skin lightened mainly through the appearance of new alleles at three genes: SLC45A2, SLC24A5, and TYRP1 (Beleza et al., 2013; Canfield et al., 2014; Soejima et al., 2005; Voight et al., 2006).”
BackgroundAdvances in integrative African genomics
Zhang, C., Hansen, M. E. B., & Tishkoff, S. A. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.09.013 · Cited by 23 · see citing works
Jones, P. R., Lucock, M. D., Chaplin, G., Jablonski, N. G., Veysey, M. J., Scarlett, C. J., & Beckett, E. (2020) · Genes & Nutrition · doi:10.1186/s12263-020-00663-3 · Cited by 24 · see citing works
“Sample set n Latitude Sample ID# Data source* Ami (Taiwan) 40 22.5–24.0° N SA000002C [35] Atayal (Taiwan) 41 21.8–25.5° N SA000021D [35] Dai (China) 10 21.0° N SA001493R [36] Daur (China) 10 48.0–49.0° N SA001488V [36] Han (China) 45 36.0–39.0° N SA001483Q [36] Hezhen (China) 10 47.0–48.0° N SA001490O [36] Japanese 29…”
BackgroundMethodInfluentialThe Genetic Overlap Between Hair and Eye Color
Lin, B. D., Willemsen, G. A. H. M., Abdellaoui, A., Bartels, M., Ehli, E. A., Davies, G. E., Boomsma, D. I., & Hottenga, J. (2016) · Twin Research and Human Genetics · doi:10.1017/thg.2016.85 · Cited by 17 · see citing works
“Peripheral pigmentation traits such as eye, hair, and skin color show a close correspondence with latitudes in national to worldwide geographic regions: lower-pigmentation prevalence is found to be higher in high latitudes (Abdellaoui et al., 2013; Beleza et al., 2013).”
Skin colour: A window into human phenotypic evolution and environmental adaptation
Liu, J., Bitsue, H. K., & Yang, Z. (2024) · Molecular Ecology · doi:10.1111/mec.17369 · Cited by 25 · see citing works
“This allele first appeared in European populations around 11–19 kya and became fixed around 5 kya, well after modern humans first arrived in Europe (Beleza et al., 2013).”
BackgroundFarré, X., Blay, N., Cortés, B., Carreras, A., Iraola‐Guzmán, S., & de Cid, R. (2023) · Genes · doi:10.3390/genes14010149 · Cited by 19 · see citing works
“The latitude hypothesis, explained by favoring vitamin D synthesis in regions far from the equator, is accepted as the main force during ancestral human population spreading [28], but not the only explanation.”
BackgroundIdentifying and Classifying Shared Selective Sweeps from Multilocus Data
Harris, A. M., & DeGiorgio, M. (2020) · Genetics · doi:10.1534/genetics.120.303137 · Cited by 20 · see citing works
Fast and accurate out-of-core PCA framework for large scale biobank dataPreprint
Li, Z., Meisner, J., & Albrechtsen, A. (2023) · Genome Research · doi:10.1101/gr.277525.122 · Cited by 19 · see citing works
Skin pigmentation variation among populations of West Maharashtra, India
Jonnalagadda, M., Ozarkar, S., Ashma, R., & Kulkarni, S. S. (2015) · American Journal of Human Biology · doi:10.1002/ajhb.22738 · Cited by 20 · see citing works
“Furthermore, selective sweeps at the SLC24A5, SLC45A2, and TYRP1 loci among Europeans likely began over the last 11,000–19,000 years (Beleza et al., 2013).”
BackgroundNutrigenomics in the context of evolution
Carlberg, C. (2023) · Redox Biology · doi:10.1016/j.redox.2023.102656 · Cited by 18 · see citing works
“increase in population size in Europe [90,91], such as the use of milk products as food source for adults and the rise of agriculture [92] (see section below).”
BackgroundTournebize, R., Poncet, V., Jakobsson, M., Vigouroux, Y., & Manel, S. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12957 · Cited by 13 · see citing works
Adding Sense: Context and Interest in a Grammar of Multimodal Meaning
Kalantzis, M., & Cope, B. (2020) · Cited by 16 · see citing works
Are Preferences for Women’s Hair Color Frequency-Dependent?
Janif, Z. J., Brooks, R. C., & Dixson, B. J. W. (2014) · Adaptive Human Behavior and Physiology · doi:10.1007/s40750-014-0008-y · Cited by 16 · see citing works
“…KITLG gene shared by Europeans and Asians began 30,000 years ago, and selective sweeps for alleles within three genes (TYRP1, SLC4A5, and SLC45A2) specific to lighter skin in Europeans occurred between 11,000 and 19,000 years ago (Beleza et al. 2013) and 6,500–4,000 years ago (Wilde et al. 2014).”
BackgroundThe color of normal: How a Eurocentric focus erases pigmentation complexity
Norton, H. (2020) · American Journal of Human Biology · doi:10.1002/ajhb.23554 · Cited by 14 · see citing works
Hudson, N. J., Neto, L. R. P., Kijas, J., McWilliam, S. M., Taft, R. J., & Reverter, A. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-66 · Cited by 13 · see citing works
“For example SLC24A5 which is associated with skin lightening in cold climate Europeans [17] Tuscans and Gujarati Indians [18] is specifically detected by CEhZ in the CEU, TSI and GIH populations (Figure 5A); HERC2 is associated with variation in eye colour in Europeans [19] and is similarly…”
BackgroundReinders, A., & Ward, J. M. (2012) · Molecular Medicine Reports · doi:10.3892/mmr.2015.3462 · Cited by 13 · see citing works
“The L374F mutation in SLC45A2 is hypothesized to have occurred recently and to have undergone positive selection during the last 5,000 years (41,42).”
BackgroundPandey, D., Harris, M., Garud, N. R., & Narasimhan, V. M. (2024) · Nature Communications · doi:10.1038/s41467-024-53852-8 · Cited by 13 · see citing works
Identifying signatures of positive selection in pigmentation genes in two South Asian populations
Jonnalagadda, M., Bharti, N., Patil, Y., Ozarkar, S., Sunitha Manjari, K., Joshi, R., & Norton, H. (2017) · American Journal of Human Biology · doi:10.1002/ajhb.23012 · Cited by 13 · see citing works
“…OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color (Basu Mallick et al., 2013; Beleza et al., 2013; Candille et al., 2012; Edwards et al., 2010; Hider et al., 2013; ; Jonnalagadda et al., 2016a; Lamason et al., 2005; Liu et al.,…”
BackgroundDissecting dynamics and differences of selective pressures in the evolution of human pigmentation
Huang, X., Wang, S., Li, J., & He, Y. (2021) · Biology Open · doi:10.1242/bio.056523 · Cited by 12 · see citing works
“KITLG were under directional selection before the divergence of ancestral Europeans and East Asians (Donnelly et al., 2012; Beleza et al., 2013).”
BackgroundResultInfluentialJorgenson, E., Choquet, H., Yin, J., Hoffmann, T., Banda, Y., Kvale, M., Risch, N., Schaefer, C., & Asgari, M. (2020) · Communications Biology · doi:10.1038/s42003-020-01461-8 · Cited by 9 · see citing works
The evolution of skin pigmentation associated variation in West EurasiaPreprint
Ju, D., & Mathieson, I. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.08.085274 · Cited by 12 · see citing works
“While the UK Biobank is well-powered to detect variation that is segregating in present-day Europeans, it may not detect variants that are no longer segregating.”
BackgroundInfluentialBoyrie, L., Moreau, C., Frugier, F., Jacquet, C., & Bonhomme, M. (2020) · Heredity · doi:10.1038/s41437-020-0349-1 · Cited by 8 · see citing works
“15_46179457 and 15_46172199) localize 465 on the same SLC24A5 haplotype background previously characterized (43-45).”
BackgroundWeasel, L. H. (2022) · The American Naturalist · doi:10.1086/720130 · Cited by 10 · see citing works
“As a result, “our knowledge of skin and eye color genetics is incomplete, based mostly on the limited range of phenotypic diversity represented by individuals of European ancestry or on candidate gene studies in African Americans” (Beleza et al. 2013, p. e1003372).”
BackgroundCasella, A., Long, C., Zhou, J., Lai, M., O’Lear, L., Caplan, I., Levine, M. A., & Roizen, J. D. (2020) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgaa056 · Cited by 10 · see citing works
Skin color variation in Africa
Tang, H., & Barsh, G. S. (2017) · Science · doi:10.1126/science.aaq1322 · Cited by 8 · see citing works
Ang, K. C., Canfield, V. A., Foster, T. C., Harbaugh, T. D., Early, K. A., Harter, R. L., Reid, K. P., Leong, S. L., Kawasawa, Y. I., Liu, D. J., et al. (2023) · eLife · doi:10.7554/elife.77514 · Cited by 6 · see citing works
“The effect size for SLC24A5 A111T measured here is consistent with previously reported results of –5 melanin units calculated from an African-American sample ( Lamason et al., 2005 ; Norton et al., 2007 ) and –5.5 from admixed inhabitants of the Cape Verde islands ( Beleza et al., 2013 ).”
BackgroundResultInfluentialKleisner, K. (2021) · Symmetry · doi:10.3390/sym13122408 · Cited by 7 · see citing works
Adaptation and co‐adaptation of skin pigmentation and vitamin D genes in native Americans
Missaggia, B. O., Reales, G., Cybis, G. B., Hünemeier, T., & Bortolini, M. C. (2020) · American Journal of Medical Genetics Part C Seminars in Medical Genetics · doi:10.1002/ajmg.c.31873 · Cited by 7 · see citing works
Duffy, D. L. (2015) · Wiley eBooks · doi:10.1002/9780470015902.a0024646 · Cited by 7 · see citing works
Artificial Intelligence in Skin Cancer: Diagnosis and Therapy
Das, T., Kumar, V., Prakash, A., & Lynn, A. M. (2021) · Springer eBooks · doi:10.1007/978-981-16-0364-8_9 · Cited by 7 · see citing works
Timmermann, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.19.049734 · Cited by 6 · see citing works
“Furthermore, I allow ss to vary in time to capture the fact that the habitat range of HS broadened as a result of mutations (Beleza et al., 2013) that occurred between 42-38 ka which allowed Eurasian HS to down-regulate melanin production, develop lighter skin and synthesize Vitamin D in higher latitudes with less sol…”
BackgroundInfluentialEstimating time to the common ancestor for a beneficial allelePreprint
Smith, J., Coop, G., Stephens, M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/071241 · Cited by 5 · see citing works
Assessment of Using Cosmetics Containing Hydroquinone among Sudanese Women
Osman, H., Shayoub, M. E. H., Ahmed, M. M. E., et al. (2015) · Journal of Cosmetics Dermatological Sciences and Applications · doi:10.4236/jcdsa.2015.52009 · Cited by 5 · see citing works
“Therefore, it had been banned in some countries like France because of fears of cancer risk [8].”
BackgroundEvolution of Skin Pigmentation Differences in Humans
López, S., & Alonso, S. (2014) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0021001.pub2 · Cited by 6 · see citing works
Ekpunobi, U. E., Okonkwo, E. O., Udeh, C. V., et al. (2014) · Cited by 5 · see citing works
Fine, A. G., & Steinrücken, M. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011769 · Cited by 6 · see citing works
“049 (CI: [0.029, 0.066]), Beleza et al. (2013) estimate s in the range of 0 .”
Influential
- Authors
- Beleza, S., Santos, A. M., McEvoy, B., Alves, I., Martinho, C., Cameron, E., Shriver, M. D., Parra, E. J., & Rocha, J.
- Affiliations
- Universidade do Porto (PT)
- QIMR Berghofer Medical Research Institute (AU)
- Pennsylvania State University (US)
- University of Toronto (CA)
- Corresponding author
- Beleza, Sandra
- Rocha, Jorge
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-08-25
- Volume
- 30
- Issue
- 1
- Pages
- 24-35
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3525146
- OpenAlex
- W2007072747
- Cited by
- 156
- References
- 73
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 5 · 2023: 15 · 2022: 6 · 2021: 8 · 2020: 22 · 2019: 7 · 2018: 10 · 2017: 17 · 2016: 10 · 2015: 13 · 2014: 20 · 2013: 10 · 2012: 3
- FWCI
- 8.82
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Funders
- Ontario Innovation Trust
- Government of Ontario
- National Institutes of Health
- Natural Sciences and Engineering Research Council of Canada
- Fundação para a Ciência e a Tecnologia (PTDC/BIA-BDE/64044/2006, PTDC/BIA-BDE/68999/2006, SFRH/BPD/21887/2005)
- National Human Genome Research Institute (R01HG002154, HG-002154)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- skin pigmentation, selective sweeps, stem cell factor, TRP-1, SLC24A5, SLC45A2, vitamin D synthesis, latitudinal gradient, out-of-Africa migration, European populations, East Asian populations, demographic expansion, microsatellite haplotypes, selection coefficients
- MeSH terms
- Africa, Alleles, Antigens, Neoplasm, DNA, Ethnicity, Europe, Haplotypes, Humans, Membrane Glycoproteins, Oxidoreductases, Phenotype, Phylogeny, Selection, Genetic, Skin Pigmentation, Antiporters, Microsatellite Repeats, Evolution, Molecular, Polymorphism, Single Nucleotide, Membrane Transport Proteins, White People, Asian People, Genetic Loci
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