Fire Haired
04-04-2014, 05:24 AM
I learned about this through a new Eurogenes thread (http://eurogenes.blogspot.com/2014/04/the-really-old-europe-is-mostly-in.html),
Davidski,
A new version of the Lazaridis et al. ancient genomes preprint has just appeared at bioRxiv
Click here (http://www.biorxiv.org/highwire/filestream/968/field_highwire_adjunct_files/2/001552-3.pdf) to see the new preprint. It is very long and has a lot of great new(and repeated) information. I want to spread the news quickly and not spend days to write a decent thread about alot of stuff i don't totally understand.
Besides Y DNA and pigmentation I saw very little difference between their previous preprint. I don't want to write anything that's not about Y DNA and pigmentation yet because i will defintley make many mistakes.
Y DNA
New Y chromosome SNP's were tested for Loschbour, Motala2, Motala3, and Motala12. Loschbour and Motala-2-3-9-12 were all tested and found to have at least one defining mutation of Y DNA I. Motala6 is L55+ so a member of Q1a2a but L232- which takes him out of Q1 so his Y DNA haplogroup is unknown. Loschbour was tested for 7 mutations that define I2a1b and had all of them, Motala12 was tested for 5 and had all of them, and Motala3 was tested for 3 and had all of them.
But there was a note that says Loschbour was missing two mutations 'considered to be phylogenetically equivalent for defining haplogroup I2a1b".
Of the SNPs considered to be phylogenetically equivalent for defining haplogroup I2a1b, Loschbour carried the ancestral state for two of them. Present-day individuals appear to be derived (Kenneth Nordtvedt, personal communication) for all these SNPs. It thus appears that Loschbour belonged to a branch of this haplogroup that lacked some of the mutations found in his closest relatives today.
Motala12 was also missing these two mutations. So possibly they belonged to a brotherclade or the ancestral version of modern I2a1b(I know i am repeating what the quote states). Motala6 did not have any I1 defining mutations that he was tested for and he did not have I2a1b alleles in SNP CTS1293(only I2a1b defining SNP he was tested for) unlike Motala12, Loschbour, and Motala3. Motala9 was tested for an I1 mutation and was negative but not for any I2(including all subclades) mutations.
Pigmentation
New SNP's associated with pigmentation were tested for Loschbour, Stuttgart, and Motala12(who was not tested at all in their previous preprint). The same 8plex and Hirisplex were listed for Loschbour and Stuttgart, but some results were also listed for Motala12.
Here are the predictions for hair and eye color of Loschbour and Stuttgart using the Hirisplex model.
<tbody>
Hair color
Loschbour
Stuttgart
Brown
41.30%
22%
Red
0%
0%
Black
57.90%
77.40%
Blond
0.80%
0.50%
Hair shade
Loschbour
Stuttgart
Light
2.20%
0.60%
Dark
97.80%
99.40%
Eye color
Loschbour
Stuttgart
Blue
61.30%
0%
Intermediate
16.60%
0.40%
Brown
22.20%
99.60%
</tbody>
Motala12(Sweden, 6,000BC) like Loschbour(Luxembourg, 6220-5990 BC) and La brana-1 (http://www.theapricity.com/forum/showthread.php?112037-La-Brana-1-had-blue-eyes-dark-skin-dark-hair-and-Y-DNA-C1a2-V20)(Spain, 5940-5690BC) most likely had light eyes and dark hair. That's 3/3 for Mesolithic Europeans which probably means that combination was widespread and very popular in Europe by at least 8,000 years ago. The most compelling evidence Motala12 also had light eyes(probably blue) is that he had G/G alleles in SNP rs12913832. Motala12 had T/T alleles in SNP rs12203592(in gene IRF4) like Loschbour and La Brana-1(T/C). Today T/T and T/C alleles in that SNP are very rare in modern Europeans and absent in east asians and Africans(see here (http://snpedia.com/index.php/Rs12203592)). IRF4 is associated with sensitivity of skin to sun exposure, freckles, blue eyes, and brown hair color(got that from here (http://en.wikipedia.org/wiki/IRF4)).
Alot of the stuff about pigmentation is new to me so I am going to give some quotes.
We typed the three ancient modern humans at 7 SNPs forming three short haplotypes associated with eye color in present-day worldwide populations (Table S8.3)26. The observed reads in the Motala12 forager, like the Loschbour forager match the blue-eye-associated allele at all 7 SNPs.
We find that the Loschbour forager is homozygous for the h-1 HERC2/OCA2 haplotype observed in 97% of blue-eyed individuals in a present-day study population from Turkey, Jordan, and Denmark.
Motala12 was tested for 10 of them and had all of them except in rs3935591 he had T/C and 97% of modern blue eyed people(and Loschbour) have C/C. Of the mutations tested and associated with non dark hair none of the ancient samples had any.
Motala12 surprisingly had alleles A/A('light skin" version) in SNP rs1426654(in gene SLC24A5) like near eastern(main ancestors migrated to Europe) farmers Stuttgart and Otzi and unlike fellow European hunter gatherers Loschbour and La Brana-1 who had G/G.
There is another similarity between Motala12, near eastern farmers, and most modern west Eurasians with SNP's associated with skin color.
Examining the SLC24A5 region, we find that the Stuttgart farmer is homozygous for the C11 haplotype found in 97% of all modern carriers of the derived rs1426654 pigmentation-lightening allele27. The A111T mutation is estimated to have arisen at ~22-28 kya28, with the selective sweep favoring its rise beginning ~19kya (under a dominant model) or ~11kya (under an additive model)29. The Loschbour forager does not carry the derived rs1426654 allele. The Motala12 forager, like the Stuttgart farmer, is homozygous for the C11 haplotype.
This means that middle eastern ancestors are not the sole source of the derived rs1426654 pigmentation-lightening allele in modern Europeans. Like i have said many times before in my opinon the skin color of these ancient hunter gatherers is unknown. A good guess is that they had dark skin, but there is evidence in modern people that they had light skin and possibly some(in eastern Europe?) who have not been sampled had non dark hair. The farmers were probably as light as Sardinians(their closest relatives), as dark as west asians, or somewhere in-between. It is pretty certain that both European hunter gatherers and near eastern farmers had primarily dark hair, but the hunter gatherers were mainly light eyed while the farmers mainly dark eyed.
Of the three mutations(in genes TYR, SLC24A5, and SLC45A2) most associated with light skin in Europe(all are just as popular in west asians except the one in gene SLC45A2 which is ~50% in west asians and ~100% in Europeans) La brana-1 had 0/3, Loschbour had 0/3, Motala12 had 1/3, Stuttgart had 2/3, and of tested Otzi had 2/2. Copper age(Yamna and Catacomb cultures) and Eneolithic people of the Pontiac steppe have been found to most likely have had around 90% brown eyes, an even higher percentage of dark hair, and possibly dark skin(click here (http://www.theapricity.com/forum/showthread.php?118795-List-of-65-ancient-Pontaic-steppe-individuals-and-DNA-results)). In contrast bronze and iron age Indo Iranians of south Siberia who are their supposed descendants and relatives had majority light eyes, light hair, and probably light skin(of SNP's associated with pigmentation tested their frequencies were no differnt from modern northern and eastern Europeans).
Davidski,
A new version of the Lazaridis et al. ancient genomes preprint has just appeared at bioRxiv
Click here (http://www.biorxiv.org/highwire/filestream/968/field_highwire_adjunct_files/2/001552-3.pdf) to see the new preprint. It is very long and has a lot of great new(and repeated) information. I want to spread the news quickly and not spend days to write a decent thread about alot of stuff i don't totally understand.
Besides Y DNA and pigmentation I saw very little difference between their previous preprint. I don't want to write anything that's not about Y DNA and pigmentation yet because i will defintley make many mistakes.
Y DNA
New Y chromosome SNP's were tested for Loschbour, Motala2, Motala3, and Motala12. Loschbour and Motala-2-3-9-12 were all tested and found to have at least one defining mutation of Y DNA I. Motala6 is L55+ so a member of Q1a2a but L232- which takes him out of Q1 so his Y DNA haplogroup is unknown. Loschbour was tested for 7 mutations that define I2a1b and had all of them, Motala12 was tested for 5 and had all of them, and Motala3 was tested for 3 and had all of them.
But there was a note that says Loschbour was missing two mutations 'considered to be phylogenetically equivalent for defining haplogroup I2a1b".
Of the SNPs considered to be phylogenetically equivalent for defining haplogroup I2a1b, Loschbour carried the ancestral state for two of them. Present-day individuals appear to be derived (Kenneth Nordtvedt, personal communication) for all these SNPs. It thus appears that Loschbour belonged to a branch of this haplogroup that lacked some of the mutations found in his closest relatives today.
Motala12 was also missing these two mutations. So possibly they belonged to a brotherclade or the ancestral version of modern I2a1b(I know i am repeating what the quote states). Motala6 did not have any I1 defining mutations that he was tested for and he did not have I2a1b alleles in SNP CTS1293(only I2a1b defining SNP he was tested for) unlike Motala12, Loschbour, and Motala3. Motala9 was tested for an I1 mutation and was negative but not for any I2(including all subclades) mutations.
Pigmentation
New SNP's associated with pigmentation were tested for Loschbour, Stuttgart, and Motala12(who was not tested at all in their previous preprint). The same 8plex and Hirisplex were listed for Loschbour and Stuttgart, but some results were also listed for Motala12.
Here are the predictions for hair and eye color of Loschbour and Stuttgart using the Hirisplex model.
<tbody>
Hair color
Loschbour
Stuttgart
Brown
41.30%
22%
Red
0%
0%
Black
57.90%
77.40%
Blond
0.80%
0.50%
Hair shade
Loschbour
Stuttgart
Light
2.20%
0.60%
Dark
97.80%
99.40%
Eye color
Loschbour
Stuttgart
Blue
61.30%
0%
Intermediate
16.60%
0.40%
Brown
22.20%
99.60%
</tbody>
Motala12(Sweden, 6,000BC) like Loschbour(Luxembourg, 6220-5990 BC) and La brana-1 (http://www.theapricity.com/forum/showthread.php?112037-La-Brana-1-had-blue-eyes-dark-skin-dark-hair-and-Y-DNA-C1a2-V20)(Spain, 5940-5690BC) most likely had light eyes and dark hair. That's 3/3 for Mesolithic Europeans which probably means that combination was widespread and very popular in Europe by at least 8,000 years ago. The most compelling evidence Motala12 also had light eyes(probably blue) is that he had G/G alleles in SNP rs12913832. Motala12 had T/T alleles in SNP rs12203592(in gene IRF4) like Loschbour and La Brana-1(T/C). Today T/T and T/C alleles in that SNP are very rare in modern Europeans and absent in east asians and Africans(see here (http://snpedia.com/index.php/Rs12203592)). IRF4 is associated with sensitivity of skin to sun exposure, freckles, blue eyes, and brown hair color(got that from here (http://en.wikipedia.org/wiki/IRF4)).
Alot of the stuff about pigmentation is new to me so I am going to give some quotes.
We typed the three ancient modern humans at 7 SNPs forming three short haplotypes associated with eye color in present-day worldwide populations (Table S8.3)26. The observed reads in the Motala12 forager, like the Loschbour forager match the blue-eye-associated allele at all 7 SNPs.
We find that the Loschbour forager is homozygous for the h-1 HERC2/OCA2 haplotype observed in 97% of blue-eyed individuals in a present-day study population from Turkey, Jordan, and Denmark.
Motala12 was tested for 10 of them and had all of them except in rs3935591 he had T/C and 97% of modern blue eyed people(and Loschbour) have C/C. Of the mutations tested and associated with non dark hair none of the ancient samples had any.
Motala12 surprisingly had alleles A/A('light skin" version) in SNP rs1426654(in gene SLC24A5) like near eastern(main ancestors migrated to Europe) farmers Stuttgart and Otzi and unlike fellow European hunter gatherers Loschbour and La Brana-1 who had G/G.
There is another similarity between Motala12, near eastern farmers, and most modern west Eurasians with SNP's associated with skin color.
Examining the SLC24A5 region, we find that the Stuttgart farmer is homozygous for the C11 haplotype found in 97% of all modern carriers of the derived rs1426654 pigmentation-lightening allele27. The A111T mutation is estimated to have arisen at ~22-28 kya28, with the selective sweep favoring its rise beginning ~19kya (under a dominant model) or ~11kya (under an additive model)29. The Loschbour forager does not carry the derived rs1426654 allele. The Motala12 forager, like the Stuttgart farmer, is homozygous for the C11 haplotype.
This means that middle eastern ancestors are not the sole source of the derived rs1426654 pigmentation-lightening allele in modern Europeans. Like i have said many times before in my opinon the skin color of these ancient hunter gatherers is unknown. A good guess is that they had dark skin, but there is evidence in modern people that they had light skin and possibly some(in eastern Europe?) who have not been sampled had non dark hair. The farmers were probably as light as Sardinians(their closest relatives), as dark as west asians, or somewhere in-between. It is pretty certain that both European hunter gatherers and near eastern farmers had primarily dark hair, but the hunter gatherers were mainly light eyed while the farmers mainly dark eyed.
Of the three mutations(in genes TYR, SLC24A5, and SLC45A2) most associated with light skin in Europe(all are just as popular in west asians except the one in gene SLC45A2 which is ~50% in west asians and ~100% in Europeans) La brana-1 had 0/3, Loschbour had 0/3, Motala12 had 1/3, Stuttgart had 2/3, and of tested Otzi had 2/2. Copper age(Yamna and Catacomb cultures) and Eneolithic people of the Pontiac steppe have been found to most likely have had around 90% brown eyes, an even higher percentage of dark hair, and possibly dark skin(click here (http://www.theapricity.com/forum/showthread.php?118795-List-of-65-ancient-Pontaic-steppe-individuals-and-DNA-results)). In contrast bronze and iron age Indo Iranians of south Siberia who are their supposed descendants and relatives had majority light eyes, light hair, and probably light skin(of SNP's associated with pigmentation tested their frequencies were no differnt from modern northern and eastern Europeans).