Friday, November 21, 2014

Google+ Awesome trick for the previous post images ...


Google+ automatically created an awesome trick motion image based on the previous post images which were uploaded. Just thought of sharing this ...

Previous Post: GEDmatch Archaic DNA matches

GEDmatch Archaic DNA matches

I would like to thank John Olson from GEDmatch for preparing an excellent tool to compare all ancient DNA uploaded to GEDmatch in one page. The tool allows to reduce the cM as low as 0.5. However, based on my experience and experiments, always try to use 1.5 to 2 cM and above.

Please note, if you see the page giving the exact same results even after changing the thresholds, make sure you refresh the page using F5 key (this seems to be a bug?).

While it is useful to compare your autosomal DNA with ancient DNA kits, it is also helpful to see how other ancient DNA matches with each other. For the below comparisions, I had used 2 cM.















Thursday, November 20, 2014

NE1 Ancient DNA Analysis

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE1 from Polgár-Ferenci-hát site in Hungary into formats familiar to genetic genealogists and uploaded here. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and uploaded to GEDmatch as kit# F999937.

Admixture

Dodecad v3

Eurogenes

MDLP


Eye Color

Eye Color


Runs of Homozygosity

RoH reveals parents of Kostenki14 are not related in their genealogical timeframe.

Mt-DNA

NE1 is a female and she belongs to mt-Haplogroup U5b2c

Archaic DNA matches

GEDmatch Archaic DNA Matches.
(Note: Browser seems to cache the image for GEDmatch's Archaic DNA matches. So, if you get same result when you change the thresholds, make sure you refresh the browser).

NE1 is so closely related to LBK. Below is at 700 SNPs / 7 cM. It has 2 matching segments at 500 SNPs / 5 cM.

NE1 and LBK.

 BR2 is also related to NE1. BR2 could possibly be a descendant of NE1.

NE1 and BR2

Ust'-Ishim could be an ancestor to NE1.

NE1 and Ust'-Ishim

Loschbour could also be an ancestor to NE1.

NE1 and Loschbour

HIrisPlex Eye and Hair Colour DNA Phenotyping

PBlueEye 0.798765
PIntermediateEye 0.078415
PBrownEye 0.12282
Full_AUC_BlueEye 0.940398
Full_AUC_IntermediateEye 0.743643
Full_AUC_BrownEye 0.94528
Numb_missingSNPs_Eye 0
Name_missingSNPs_Eye
AUC_Loss_BlueEye 0
AUC_Loss_IntermediateEye 0
AUC_Loss_BrownEye 0
PBlondHair 0.052597
PBrownHair 0.401653
PRedHair 0.000564
PBlackHair 0.545185
Full_AUC_BlondHair 0.810616
Full_AUC_BrownHair 0.751061
Full_AUC_RedHair 0.922712
Full_AUC_BlackHair 0.848114
Numb_missingSNPs_Hair 3
Name_missingSNPs_Hair rs86insA_A / Y152OCH_A / rs2228479_A
AUC_Loss_BlondHair 0.004374
AUC_Loss_BrownHair 0.002165
AUC_Loss_RedHair 0.010717
AUC_Loss_BlackHair 0.002165
PLightHair 0.154469
PDarkHair 0.845531
Full_AUC_HairShade 0.905444
Numb_missingSNPs_HairShade 1
Name_missingSNPs_HairShade rs2228479_A
AUC_Loss_HairShade 0.000133

S. Walsh, L. Chaitanya, L. Clarisse, L. Wirken, J. Draus-Barini, L. Kovatsi, H. Maeda, T. Ishikawa, T. Sijen, P. de Knijff, W. Branicki, F. Liu, M. Kayser, Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage. Forensic Science International: Genetics. Submitted. 

According to HIrisPlex, NE1 had Blue hair and Brownish/Black hair.


Kit in FTDNA Database


NE1 has matches in FTDNA. I want to thank Roberta and FTDNA for helping to unlock ancient DNA kits.

Matches in FTDNA

Ust'-Ishim Ancient DNA has matches with living people!

The authors provided a high-quality genome sequence of a 45,000-year-old modern human from Siberia. I converted this raw data of Ust'-Ishim into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999935. I also transferred the kit to FTDNA. Interestingly, the 45000 year old sample as mentioned by authors is having matches with living people as recent cousins.

GEDmatch Matches

There are several matches in GEDmatch.
Matches at 500 SNPs / 5 cM

FTDNA Matches

FamilyTreeDNA has 1 match.
Matches in FTDNA


Do you have any matching segments?

Related  BlogUst'-Ishim Ancient DNA Analysis

Wednesday, November 19, 2014

Kostenki14 Ancient DNA Analysis

The origin of contemporary Europeans remains contentious. The authors obtained a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. I converted this raw data of Kostenki 14 into formats familiar to genetic genealogists and uploaded here. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999936.

Admixture

Dodecad v3

Eurogenes

MDLP


Eye Color



Runs of Homozygosity

RoH reveals parents of Kostenki14 are not related in their genealogical timeframe.

Y-DNA and mt-DNA

Y-Haplogroup is C-V199 and mt-Haplogroup is U2b

Archaic DNA matches

K14 seems to be closer to Ust'-Ishim/LBK/Loschbour than other ancients when viewed at 1 cM/ 100 SNPs in GEDmatch.

Comparison to other Ancient samples.

Triangulated Ancient DNA Segments

The segment Chr8: 51067154 - 52075739 has 197 SNPs / 1 Mb which occurs in all Loschbour, BR2, Kostenki14, NE1 ancient DNA samples. Based on other autosomal segment matches, below is how all 4 ancients are related through autosomal DNA. "Loschbour/BR2/Kostenki14/NE1" means, the common ancestor for all 4 ancient DNA samples.


GEDmatch 1-to-many

K14 does have matches with living people around less than 10.
Matches in GEDmatch