Brace, Selina; Diekmann, Yoan; Booth, Thomas J.; Faltyskova, Zuzana; Rohland, Nadin; Mallick, Swapan; Ferry, Matthew; Michel, Megan et al.. (2019). «Ancient genomes indicate population replacement in Early Neolithic Britain» Nature Ecology & Evolution 3 (5): 765–771. doi:10.1038/s41559-019-0871-9. OCLC.6520225PMID30988490.. Supplementary Material (p.18-19): "This individual has light or blue/green eye colour, it is not light blue, there are elements of brown/yellow in the eye to give a proposed perceived green colour. Better coverage at the low sequenced marker would clarify this but blue/hazel cannot be ruled out. It is certainly not a brown eyed or clear blue-eyed individual...
Skin pigmentation
[assumptions about missing information omitted] The following range for skin pigmentation prediction is possible for this individual with these parameters:...
Intermediate 0.152 - 0.038
Dark-Black 0.848 - 0.962
Final prediction: Dark/Dark-to-Black skin
If we omit the three missing alleles, our tool produces 0.752 and 0.248 probabilities for the intermediate and dark-black category respectively, changing the prediction ranges to 0.752- 0.038 and 0.248-0.962. However, note that this completely removes the locus from the prediction model; hence the prediction will not perform optimally (how the prediction model was made). It is therefore best to have some allele present to infer the most probable range for Cheddar Man and we derive the ranges above from the extreme allele constellations only.
Explanation: The missing loci certainly impact on this prediction; however, utilizing the input of all ancestral alleles is the preferred option over the use of the derived alleles at these loci – hence 0.152 for intermediate and 0.848 for Dark-to-Black would be the most probable profile. That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci. Also, this effect of skipping a skin pigmentation prediction category with regards probability values, tends to be observed more often in admixed individuals. What is important to note is the input of the dark-black prediction is significant on the intermediate category and therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is present. It is unlikely that this individual has the darkest possible pigmentation, but it cannot be ruled out. Better sequencing coverage would clarify to what degree this individual has a dark complexion."
Haak, Wolfgang; Lazaridis, Iosif; Patterson, Nick; Rohland, Nadin; Mallick, Swapan; Llamas, Bastien; Brandt, Guido; Nordenfelt, Susanne et al.. (10 February 2015). «Massive migration from the steppe is a source for Indo-European languages in Europe» Nature 522 (7555): 207–211. doi:10.1038/nature14317. OCLC.5048219PMID25731166. Bibcode: 2015Natur.522..207H..
Haak, Wolfgang; Lazaridis, Iosif; Patterson, Nick; Rohland, Nadin; Mallick, Swapan; Llamas, Bastien; Brandt, Guido; Nordenfelt, Susanne et al.. (10 February 2015). «Massive migration from the steppe is a source for Indo-European languages in Europe» Nature 522 (7555): 207–211. doi:10.1038/nature14317. OCLC.5048219PMID25731166. Bibcode: 2015Natur.522..207H..
Brace, Selina; Diekmann, Yoan; Booth, Thomas J.; Faltyskova, Zuzana; Rohland, Nadin; Mallick, Swapan; Ferry, Matthew; Michel, Megan et al.. (2019). «Ancient genomes indicate population replacement in Early Neolithic Britain» Nature Ecology & Evolution 3 (5): 765–771. doi:10.1038/s41559-019-0871-9. OCLC.6520225PMID30988490.. Supplementary Material (p.18-19): "This individual has light or blue/green eye colour, it is not light blue, there are elements of brown/yellow in the eye to give a proposed perceived green colour. Better coverage at the low sequenced marker would clarify this but blue/hazel cannot be ruled out. It is certainly not a brown eyed or clear blue-eyed individual...
Skin pigmentation
[assumptions about missing information omitted] The following range for skin pigmentation prediction is possible for this individual with these parameters:...
Intermediate 0.152 - 0.038
Dark-Black 0.848 - 0.962
Final prediction: Dark/Dark-to-Black skin
If we omit the three missing alleles, our tool produces 0.752 and 0.248 probabilities for the intermediate and dark-black category respectively, changing the prediction ranges to 0.752- 0.038 and 0.248-0.962. However, note that this completely removes the locus from the prediction model; hence the prediction will not perform optimally (how the prediction model was made). It is therefore best to have some allele present to infer the most probable range for Cheddar Man and we derive the ranges above from the extreme allele constellations only.
Explanation: The missing loci certainly impact on this prediction; however, utilizing the input of all ancestral alleles is the preferred option over the use of the derived alleles at these loci – hence 0.152 for intermediate and 0.848 for Dark-to-Black would be the most probable profile. That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci. Also, this effect of skipping a skin pigmentation prediction category with regards probability values, tends to be observed more often in admixed individuals. What is important to note is the input of the dark-black prediction is significant on the intermediate category and therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is present. It is unlikely that this individual has the darkest possible pigmentation, but it cannot be ruled out. Better sequencing coverage would clarify to what degree this individual has a dark complexion."
Haak, Wolfgang; Lazaridis, Iosif; Patterson, Nick; Rohland, Nadin; Mallick, Swapan; Llamas, Bastien; Brandt, Guido; Nordenfelt, Susanne et al.. (10 February 2015). «Massive migration from the steppe is a source for Indo-European languages in Europe» Nature 522 (7555): 207–211. doi:10.1038/nature14317. OCLC.5048219PMID25731166. Bibcode: 2015Natur.522..207H..
Malmström, H; Gilbert, MT; Thomas, MG. (November 2009). «Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians» Current Biology 19 (20): 1758–62. doi:10.1016/j.cub.2009.09.017. PMID19781941..
worldcat.org
Brace, Selina; Diekmann, Yoan; Booth, Thomas J.; Faltyskova, Zuzana; Rohland, Nadin; Mallick, Swapan; Ferry, Matthew; Michel, Megan et al.. (2019). «Ancient genomes indicate population replacement in Early Neolithic Britain» Nature Ecology & Evolution 3 (5): 765–771. doi:10.1038/s41559-019-0871-9. OCLC.6520225PMID30988490.. Supplementary Material (p.18-19): "This individual has light or blue/green eye colour, it is not light blue, there are elements of brown/yellow in the eye to give a proposed perceived green colour. Better coverage at the low sequenced marker would clarify this but blue/hazel cannot be ruled out. It is certainly not a brown eyed or clear blue-eyed individual...
Skin pigmentation
[assumptions about missing information omitted] The following range for skin pigmentation prediction is possible for this individual with these parameters:...
Intermediate 0.152 - 0.038
Dark-Black 0.848 - 0.962
Final prediction: Dark/Dark-to-Black skin
If we omit the three missing alleles, our tool produces 0.752 and 0.248 probabilities for the intermediate and dark-black category respectively, changing the prediction ranges to 0.752- 0.038 and 0.248-0.962. However, note that this completely removes the locus from the prediction model; hence the prediction will not perform optimally (how the prediction model was made). It is therefore best to have some allele present to infer the most probable range for Cheddar Man and we derive the ranges above from the extreme allele constellations only.
Explanation: The missing loci certainly impact on this prediction; however, utilizing the input of all ancestral alleles is the preferred option over the use of the derived alleles at these loci – hence 0.152 for intermediate and 0.848 for Dark-to-Black would be the most probable profile. That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci. Also, this effect of skipping a skin pigmentation prediction category with regards probability values, tends to be observed more often in admixed individuals. What is important to note is the input of the dark-black prediction is significant on the intermediate category and therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is present. It is unlikely that this individual has the darkest possible pigmentation, but it cannot be ruled out. Better sequencing coverage would clarify to what degree this individual has a dark complexion."
Haak, Wolfgang; Lazaridis, Iosif; Patterson, Nick; Rohland, Nadin; Mallick, Swapan; Llamas, Bastien; Brandt, Guido; Nordenfelt, Susanne et al.. (10 February 2015). «Massive migration from the steppe is a source for Indo-European languages in Europe» Nature 522 (7555): 207–211. doi:10.1038/nature14317. OCLC.5048219PMID25731166. Bibcode: 2015Natur.522..207H..
