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Post by Admin on Feb 21, 2018 18:59:20 GMT
Genomic Contamination Estimates To obtain a direct estimate of contamination in the nuclear data, we screened for heterogeneity in the nucleotides among X chromosome overlapping reads (discarding C to T and G to A changes attributable to DNA damage [22]). In the 204,207 nucleotide positions covered by at least two reads in La Braña 1, 341 (0.166%) showed conflicting nucleotides; in the 11,012 positions covered by three or more reads, the figure was 0.4%. In La Braña 2, there was heterogeneity in 143 of the 67,623 nucleotides covered by three or more reads, yielding a similar figure of 0.2% of potential contamination. Less numerous Y chromosome heterogeneities in two or more reads (91 out of 21,203 nucleotides and 31 out of 8,567 for La Braña 1 and 2, respectively) yielded similar values (0.4% and 0.36%). These contamination figures are overestimates, because sequencing errors are likely included in the existing reads. Mesolithic Genetic Affinities Previous studies of ancient mtDNA have shown that U5 haplotypes were common among Mesolithic Europeans, especially in Central and Eastern parts of Europe. For instance, a high incidence of U5 haplotypes (about 65%) has been detected in hunter-gatherer individuals from various sites across central and Eastern Europe [14]. U5b haplotypes have also been reportedly recovered from Mesolithic skeletons found in Aizpea in Navarra, Spain (dated to about 6,600 years before present) [32] and Reuland-Loschbour in Luxembourg (dated to about 6,000 years BC) [33], as well as from the skeleton known as “Cheddar Man” that was found in Gough's Cave, England [34]. Although no detailed methodological information has been reported for these two latter studies, the fact that the haplotype found in the mtDNA HVR1 is 16192T-16270T (without the U5a-defining nucleotide 16256T), seems to indicate that the haplotype is in fact U5b, not U5a as reported in both cases [33, 34]. U5b haplotypes are thus present in 9 out of 16 Mesolithic sites with genetic information available (56.3%), comprising 12 of the 27 individuals so far analyzed (44.4%). This surprisingly widespread presence of U5b includes present day Lithuania (Donkalnis and Kretuonas sites), Poland (Dudka site), Germany (Hohlenstein-Stadel and Falkensteiner Höhle sites), likely Luxembourg (Reuland-Loschbour site) and England (Gough's Cave), and Spain (Figure 4). Figure 4. Evidence of Genetic and Cultural Uniformity during the European Mesolithic Period Black circles, Mesolithic sites with ornaments; white circles, Mesolithic sites with perforated red deer canines (including La Braña site); squares, Mesolithic sites with genetic data; blue squares, U4 and U5 mtDNA lineages; red squares: U5b haplotypes (including La Braña site). It is generally accepted that the most ancient European mitochondrial haplogroup, U5, arose in Europe [6]. The coalescence time estimate from molecular data for the U5 is ∼25–30 thousand years (ky) and for its subhaplogroups U5a and U5b ∼16–20 and ∼20–24 ky, respectively [35]. The time estimate for U5b1c is 12.8 ky [35]. U5 haplotypes are also found in Neolithic and present day populations, although their frequency is moderated as compared to the Mesolithic, ranging from about 1% in some places along the Mediterranean up to 5%–8% in continental Europe [14]. The exceptions to this trend are the Saami populations, in northern Scandinavia, where haplogroup U5 (and mainly subhaplogroup U5b) ranges from 26.5% to 56.8%, depending on the population [36].
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Post by Admin on Feb 22, 2018 18:41:46 GMT
The genetic uniformity of the European Mesolithic hunter-gatherers that apparently carried U5 haplotypes in very high frequencies is surprising, considering the time span and also the vast geographic area involved, enlarged now with these two new haplotypes from the Iberian Peninsula. This suggests minimal geographic structure across Europe during the Mesolithic. The fact that all Mesolithic mtDNA haplotypes so far described derive from the U haplogroup suggests a common origin for the Mesolithic foragers, probably deriving from a small founding population. Being hunter-gatherers and thus highly mobile groups probably prevented the generation of any geographical structure, at least in continental Europe. La Braña 2 specimen was found with typical Mesolithic personal ornaments, consisting in 24 perforated atrophic red deer canines that were used embroidered on a cloth. The widespread presence of these perforated red deer canines in other Mesolithic sites, but especially in those from Central and Northern Europe [37, 38], suggests that La Braña individuals had tight cultural affinities with those distant regions (Figure 4). It is not known, however, if this genetic uniformity observed during the Mesolithic is a trait shared with the Upper Paleolithic modern human populations or if it is a specific feature from this period. In any case, the posterior European population affinities during the Neolithic seems to be much more complex and heterogeneous, involving probably spatial and temporal demographic movements likely related to the strategies of food production [17]. It is noteworthy that this latter scenario also received the highest support using a serial coalescent framework and Approximate Bayesian Computation (Figure S4; Supplemental Experimental Procedures). In the genomic analysis, it is interesting to see that the La Braña individuals do not cluster with modern populations from Southern Europe, including those from the Iberian Peninsula. The first PC separates a north-south distribution, whereas the second follows a general east-west pattern in modern Europeans. The position of La Braña individuals in the 1000 Genomes Project data and the 1KGPomni-chip PCAs suggests that the uniform Mesolithic substrate could be related to modern Northern European populations but may represent a gene pool that is no longer present in contemporary Southern European populations. In the latter PCA, where the origin of each Iberian sample is known, it is possible to see that the Mesolithic specimens are not related to modern Basques, contrary to what has been previously suggested in some recent studies [39]. Ancient genomics from Neolithic individuals from Scandinavia [18] supports that the spread of agriculture into Europe involved the expansion of populations from the Middle East that eventually assimilated the contemporaneous hunter-gatherers. Modern European populations seem to derive essentially from those Neolithic migrants [18]. Until now, however, the genetic affinities of the Mesolithic populations to the modern Europeans were largely unknown. Our partial La Braña 1 and 2 genomic data show that modern Iberian populations are not descendants of the local hunter-gatherers inhabiting the same region prior to the arrival of farmers and thus support a genetic shift in that region between the Mesolithic and modern populations. Current Biology, Volume 22, Issue 16, 21 August 2012, Pages 1494-1499
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Post by Admin on Feb 28, 2018 19:01:48 GMT
How can DNA survive 10,000 years? DNA can survive in bones and teeth for extraordinary lengths of time given the right environmental conditions. The oldest ancient DNA extracted to date is probably that from a horse bone which was preserved in the Canadian permafrost for over 550,000 years1. DNA survives less well in bones from temperate environments, but cave environments seem to provide some protection. Ancient DNA has been successfully extracted and analysed from 35,000 year-old human remains from Europe2. The good preservation of the DNA we retrieved from Cheddar Man is unusual, but not unexpected. How do you know his skin colour? We were able to extract enough information from Cheddar Man’s DNA to run it through a forensic tool that predicts differences in the level of skin pigmentation in modern world populations3. The results indicated that Cheddar Man’s skin pigmentation was most likely in one of the two most highly-pigmented of five categories ('dark' or 'dark to black'), and definitely not in the lightest categories. Is this a surprising finding? No, not really. Previous studies of DNA from Mesolithic individuals recovered from Spain, Luxembourg and Hungary identified that they also lacked the versions of genes associated with reduced skin pigmentation in modern, light-skinned Europeans4-6. We found that Cheddar man belonged to the same population as these individuals – usually referred to as western European Mesolithic hunter-gatherers – so in that context his pigmentation is not unusual. However, we did predict how dark Cheddar Man’s skin was by examining variation in a wider range of genes related to skin pigmentation. Will these findings be published in a peer-reviewed paper? We are preparing a related paper for submission, but this paper is not exclusively about Cheddar Man. As previous studies had already suggested that darker skin pigmentation was common in western European Mesolithic hunter-gatherers, the results from Cheddar Man are not novel enough by themselves to form the basis of a scientific paper. But finding that he was typical of that population was novel, and when put in the context of subsequent migrations into Britain, his genome becomes a valuable piece of the British population history jigsaw. Cheddar Man's skin pigmentation SNPs: rs1426654(G;G) ---> G is darker skin, modern Northern Europeans have A;A here rs16891982(C;C) ---> C allele is darker skin, also 7x more likely to have black hair rs1408799(C;C) ---> C is lighter pigmentation & higher skin cancer risk in Europeans (per SNPedia) rs1834640(A;A) --> associated with skin pigmentation (modern Europeans have A;A too) rs1800414(A;A) ---> G associated with East Asian type light skin, Non-Asians have A rs885479(G;G) ---> A associated with East Asian type light skin, Non-Asians have G rs12203592(T;T) ---> T associated with less tanning ability, common in Irish people rs1015362(G;G) ---> G associated with less tanning ability, Sub-Saharans have A;A Cheddar Man's hair & eye pigmentation: rs1667394(A;A) ---> A;A is blond hair and blue eyes 4x more likely rs12896399(G;G) ---> G;G genotype associated with lighter hair color rs12913832(G;G) ---> people with G;G blue eye color 99% of the time rs12203592(T;T) ---> T causes lighter hair & eyes, less tanning ability rs1800401(C;C) ---> C associated with blue/gray eyes possibility rs1800407(G;G) ---> G associated with blue/gray eyes possibility rs7495174(A;A) ---> A associated with blue/gray eyes more likely
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Post by Admin on Mar 1, 2018 18:52:27 GMT
Is Cheddar Man actually an escaped slave or a tourist from Africa? No! The bones of Cheddar Man have been radiocarbon dated twice, and on both occasions the results indicate that he died around 10,000 years ago7. Are there any people with lighter skin pigmentation at this time? Yes. Populations with the versions of genes primarily responsible for lighter skin pigmentation were living in parts of Scandinavia and western Asia at around the time Cheddar man was alive5,8-9. How did Europeans develop paler skin? The versions of the genes primarily responsible for lighter skin pigmentation in modern North-West Europeans arrive in Europe on the back of two waves of migration thousands of years after Cheddar Man died; one associated with Near Eastern farmers and another with pastoralists from the Pontic steppe10-12. In addition, there seems to have been ongoing natural selection favouring lighter skin pigmentation in Europe over the last 9,000 years, probably in relation to an increased need for UV induced vitamin D synthesis in the skin. What is his mitochondrial DNA type? Cheddar Man’s mitochondrial DNA, which is inherited exclusively down the maternal line, belongs to haplogroup U5b1. As this is only a tiny portion of an individual’s genome, and there have been several large-scale population movements in Europe and across the world since Cheddar Man was alive, this result has no relevance to his skin pigmentation, and says little about the distribution of this mitochondrial haplogroup amongst modern populations. How do we calculate that 10% of British ancestry can be linked to Cheddar Man? When we look at genetic variation in modern British people today, we find that – for those who do not have a recent history of migration – around 10% of their ancestry can be attributed to the ancient European population to which Cheddar Man belonged. This group is referred to as the western European Mesolithic hunter-gatherers. However, this ancestry does not relate specifically to Cheddar Man or the Mesolithic population of Britain. Well after Cheddar Man’s death, two large-scale prehistoric migrations into Britain produced significant population turnovers13. Both of these migrations into Britain represented westward extensions of population movements across Europe10-12. In both cases, these migrating populations intermixed with local people who carried western European Mesolithic hunter-gatherer ancestry, as they moved across Europe. When these populations arrived in Britain they already had some hunter-gatherer ancestry derived from this mixing with local populations. Therefore the majority of western European Mesolithic hunter-gatherers ancestry that we see in modern British people probably originates from populations who lived all over Europe during the Mesolithic, which was carried into Britain by these later migrations.
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Post by Admin on Mar 3, 2018 18:46:38 GMT
Pigmentation Susan Walsh, Manfred Kayser La Braña (Spain, Mesolithic) Eye colour —All loci are present and have good coverage. Blue eye 0.459 Int. eye 0.155 Brown eye 0.387 Final prediction: Intermediate (hazel/green) eye colour Explanation: All probabilities are less than 0.5 so it is a combination of all categories, as brown is relatively high, it is more than likely a light hazel eye colour individual, but perceived green (blue/yellow) cannot be ruled out. Hair colour—There is 1 locus (TYRP1 rs683) with low coverage (1x), hence a heterozygote is possible. Prediction is a range that includes what the 1x coverage found (derived G allele) and the possibility of an A ancestral allele being present. TYRP1 rs683 TYRP1 rs683 (homozygote GG)(heterozygote GA) Blond 0.018 0.014 Brown 0.612 0.595 Red 00 Black 0.37 0.391 Light 0.033 0.025 Dark 0.967 0.975 Prediction range: Brown 0.612 – 0.595 Black 0.37 – 0.391 Final Prediction: Black/Dark Brown hair colour Explanation: The probability value of black is >0.25 so it has a significant impact on prediction, and will darken the high brown probability. This individual would be perceived to have black hair. Dark Brown however cannot be ruled out. Skin pigmentation—Only 1 locus (BNC2 rs10756819) is missing, however the profile does contain 3 loci with low coverage (n=1x), hence a heterozygote is possible. When factoring in possible genotype combinations, a prediction range has been generated. The range consists of assuming the 3 loci with low coverage are correct as homozyogote for their sequenced allele (ASIP rs1667394 A allele (derived), OCA2 rs1545397 A allele (ancestral), TYRP1 rs683 A allele (ancestral)) and omitting BNC rs10756819 in the prediction model as it has no coverage, to including this marker with a homozygote ancestral G allele and also derived A allele. The following range for skin colour prediction is possible for this individual with these parameters: Omitting rs10756819 G ancestral allele A derived allele Very Pale 0 0 0 Pale 0 0 0 Intermediate 0.174 0.042 0.205 Dark 0.463 0.209 0.435 Dark-Black 0.363 0.749 0.360 Prediction range: Very Pale 0 Pale 0 Intermediate 0.042 - 0.205 Dark 0.209 - 0.435 Dark-Black 0.749 - 0.36 Final prediction: Dark/Dark-to-Black skin Explanation: The combined effect of probabilities in the dark and dark-to-black colour categories provide an indication that the individual has darkly pigmented skin, it is unlikely that this individual has the darkest possible skin pigmentation, however, it cannot be ruled out as the missing marker does influence that detail, but certainly skin colour is dark in complexion.
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