HVR1 and HVR2 for LBK ancient DNA matches with living people!

October 13, 2014, 10:28 pm

≫ Next: Hinxton-3 Analysis

≪ Previous: Convert Ancient DNA Sequence Reads to VCF format

$

0

0

I was investigating the mitochondria of ancient DNA samples and I am amazed to find that the 7500 year old Linearbandkeramik (LBK) sample matches exactly on HVR1 and HVR2 with several living people. I already discussed about this ancient DNA sample having matches with living people in GEDMatch earlier but adding to this, it is also matching exactly on HVR1 and HVR2 with living people.

I will discuss in this post by taking one such match. On FMS, the genetic distance is 6 and all mutations are on coding region for DQ523629. Below are the mutations in rCRS for both LBK and DQ523629.

LBK:

HVR1: 16126C 16292T 16294T (16519C)

HVR2: 73G 146C 152C 263G 279C
CR: 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 5187T 6261A 6340T 7028T 7873T 8697A 10463C 10822T 11251G 11719A 11812G 11914A 13368A 14233G 14766T 14905A 15326G 15452A 15607G 15928A

DQ523629

HVR1: 16126C 16292T 16294T (16519C)

HVR2: 73G 146C 152C 263G 279C
CR: 709A 750G 1438G 1888A 2706G 3107C 4216C 4769G 4917G 5187T 6261A 7028T 7679C 7873T 8697A 8860G 10463C 10822T 11251G 11719A 11812G 13368A 14233G 14766T 14905A 15326G 15452A 15607G 15784C 15928A


Based on FamilyTreeDNA's Understanding Your mtDNA HVR1& HVR2 Results, a HVR1 and HVR2 match means, the common ancestor is within 28 generations back (or 700 years) at 50% confidence level.

If you look carefully, LBK had 2 new mutations not found in DQ523629 while DQ523629 had 4 new mutations not found in LBK. This means, the common ancestor is 4 mutations away from DQ523629 and 2 mutations away from LBK.

mt-DNA Mutations

Matches in FamilyTreeDNA project

Looking up on T_FMS project, there are 4 exact matches for HVR1 and HVR2.

• 107961 (T2c2)
• 10814 (T2c2)
• N9023 (T2c2)
• N61893 (T2c2)

The above 4 FTDNA kits have exact matches in HVR1 and HVR2. If they are willing to share their coding region, then it would be extremely great for comparing with this ancient DNA.

Conclusion

Based on autosomal DNA which matches living people and also mitochondria HVR1 and HVR2 which again matches with living people, which could mean the sample may be within 700-1500 years back. I am happy to hear how it can be 7500 years older and still genetically match with living people on both autosomal and mtDNA as younger.

---

Hinxton-3 Analysis

October 14, 2014, 5:55 pm

≫ Next: Ancient DNA upload files update

≪ Previous: HVR1 and HVR2 for LBK ancient DNA matches with living people!

$

0

0

I was processing the Hinxton-3 over the last few days and I am finally able to complete it today. I am happy to say it did had enough SNPs to upload to GEDMatch and I uploaded it as kit# F999922.

Admixture

MDLP K23b admixture for Hinxton-3 sample

Eurogenes K13 admixture for Hinxton-3 sample

Parent's Relationship

Based on Runs of Homozygosity, parents of Hinxton-3 are related as second cousins.

Eye Color

Eye Color in GEDMatch

Telomere Length

The average telomere length based on 10 runs is 1.367  which suggests she is in her 70s when she died.

Telomere length of 1.367 for Hinxton-3 sample (Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Mt-DNA Analysis

Mitochondria haplogroup is K1a4a1a2b and the closest individual I can find so far is JQ701810 from the publicly available FMS samples.

New mutations in JQ701810 : T1189C, G5460A, A6752G, T9698C, C16189T, G5460A, A6752G
New mutations in Hixton-3: A4704G, C16184A, C16190T
Genetic Distance between these two individuals is 10 which is based on HVR1, HVR2 and CR.

The closest individual from FamilyTreeDNA projects is from mtDNA Haplogroup K (Katrine's Clan) project, FTDNA kit# 84833 for HVR1 and HVR2 comparisons who has a genetic distance of 7. Kit# 84833 is two HVR1 mutations and one HVR2 mutation away from the common ancestor with Hinxton-3 sample, while the sample is two HVR1 mutations and two HVR2 mutation away from the common ancestor.

The kit is available for 1-to-1 comparison. Please wait for atleast 2 days before checking for 1-to-many as batch processing is not yet complete. Let me know what you find.

Ancient DNA upload files update

October 15, 2014, 7:42 pm

≫ Next: How to compare Ancient DNA with yours?

≪ Previous: Hinxton-3 Analysis

$

0

0

I got notified regarding the noise and duplicate SNPs in some of the upload files. I went ahead and investigated why is that the case. Because I merged the processed files from several sequence runs into one file, there seems to be a few negligible number of SNPs having different values in different runs and gets duplicated in the final file.

Below are the samples affected which are merged from multiple runs.

• Gökhem5
• Hinxton-1
• Hinxton-2
• Hinxton-3
• Ire8 and 
• StoraFörvar11

To solve this issue, I combined all the files processed from each run and took the genotype for those SNPs which occurs the most. The processed files for each run are untouched and can be accessed at the download links. Then file is then sorted by coordinates and re-uploaded. I also uploaded the filtered version having SNPs tested by DNA companies. I also re-upload Hinxton-2 and Hinxton-3 into GEDMatch with same kit number, i.e, F999921 and F999922 respectively.

Now, the files will have much less noise and properly sorted by coordinates. Future uploads will also follow the same procedure to make sure the uploads are with less noise and easy to use with sorted coordinates.

How to compare Ancient DNA with yours?

October 17, 2014, 10:06 am

≫ Next: Ajvide58 DNA Analysis

≪ Previous: Ancient DNA upload files update

$

0

0

This is a small tutorial to compare your DNA with any of the ancient DNA with extremely low thresholds using Autosomal Segment Analyzer.

Open the Autosomal Segment Analyzer and wait until the map gets loaded (it will take a while on slow computers). Now, click File -> Open Files.

Open Files

Ancient DNA Settings

• Do not tick 'Match no-calls'. Ancient DNA may have several no calls. So, don't check it.
• Make sure Error radius is always -1. This will ensure the segment has no errors.
• For SNP Threshold, you are free to put any low number of SNPs here. E.g., 10 SNPs
• For cM Threshold, you are free to put any low decimal here. E.g, 0.1 cM
• You can tick 'Ignore SNPs which are universal matches among populations'. Example, if only AA and AC is found among populations, then that SNP is a universal match. Hence, it will not be counted towards SNP count threshold.
• Universal SNP match threshold can be tuned as well. For example, all universal matches have probability of 1. For example, if populations have AA, AC and CT, you have CT and it occurs so widely that the probability of that genotype occurrence is 75%, then you can ignore them towards SNP count by reducing the threshold to 0.60, thus further increasing the accuracy.

Matching Segments

Based on SNP/cM thresholds, when a segment matches, it will tell you in the status bar, how many accidental matches can occur for that segment, and gives you a clear picture of what is IBS noise and what are compound segments.

Once, you click 'OK', it will take a while for the processing to complete.

The output on the left pane has segment probability. On the right side, you have the probability of occurrence of the genotype for each SNP. The status will tell you if an accidental match can occur or not and even even tell you at what rate accidental matches can occur for that segment.

So, what does it mean? Any matching segment with says in description 'Accidental matches cannot occur', it means, the segment is compound and that ancient DNA does share the DNA segment through endogamy or cousin marriages. However, this does not mean you are related in any recent genealogical times. The IBS compound segment with low threshold could be thousands of years back in time. This tool only differentiates IBS noise from IBS compound segments at extremely low thresholds.

Let me know how you match compound segments or population matches with Ancient DNA.

Ajvide58 DNA Analysis

October 18, 2014, 1:13 am

≫ Next: Hinxton-4 DNA Analysis

≪ Previous: How to compare Ancient DNA with yours?

$

0

0

The authors had generated between 0.01 to 2.2-fold genome wide coverage for 6 neolithic hunter-gathers from pitted ware culture, 4 neolithic farmers from funnel beaker culture and 1 late Mesolithic hunter-gatherer. I converted the raw data of Ajvide58 from Pitted Ware Culture excavated in Sweden into formats familiar to genetic genealogists and uploaded here. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch as kit# F999924. The kit is tokenized and available for 1-to-1 comparision. Please wait a couple of days before checking for 1-to-many matches.

Admixture results

MDLP K23b Admixture Calculator

Dodecad V3 Admixture Calculator

Eurogenes K13 Admixture Calculator

Eye Color

Runs of Homozygosity

RoH reveals the the parents of Ajvide58 are 3rd cousins.

Telomere

The average length of telomere from all runs reveal it had 3.0857 which means the Ajvide58 died around the age of 35.

Telomere length of 3.057 kb relates to age 35.

Mt-DNA

Mitochondria haplogroup is U4d.

Y-DNA

The Y-Haplogroup is I-CTS772.

Hinxton-4 DNA Analysis

October 19, 2014, 4:43 pm

≫ Next: Hinxton5 Ancient DNA Analysis

≪ Previous: Ajvide58 DNA Analysis

$

0

0

I was processing the Hinxton-4 over the last few days and I am finally able to complete it today. I am happy to say it did had enough SNPs to upload to GEDMatch and I uploaded it as kit# F999925.

Admixture

MDLP K23b for Hinxton-4

Dodecad V3 for Hinxton-4

Eurogenes K13 for Hinxton-4

Runs of Homozygosity

RoH reveals the parents of Hinxton-4 are not related in his genealogical timeframe.

Eye Color

Telomere

The average length of telomere length from all runs is 2.24 kb, which means, Hinxton-4 died around the age 55.

Telomere length of 2.24 relates to age ~55 (Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Mt-DNA

Mitochondria haplogroup is H1ag1

y-DNA

Y-Haplogroup is R1b1a2a1a2c1g2a1 (R-DF25).


The kit# F999925 is available for 1-to-1 comparison. Please wait for a couple of days before doing 1-to-many comparison.

Hinxton5 Ancient DNA Analysis

October 22, 2014, 5:08 pm

≫ Next: Hinxton-4 has X-Matches with living people

≪ Previous: Hinxton-4 DNA Analysis

$

0

0

Hinxton5 is uploaded to GEDMatch as kit# F999926. More info on this sample can be found here.

Admixture

Admixture: MDLP

Sample admixture from MDLP, you can look for other admixtures like Dodecad, Eurogenes, Harappaworld from GEDMatch using the kit number F999926.

Eye Color

Eye Color for Hinxton5

Telomere

The telomere length of 0.756 suggests she is in her extreme old age, probably in her 100s.

Telomere length of 0.756 relates to age above 100. (Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Runs of Homozygosity

RoH reveals Hinxton5's parents were half-siblings.

Mt-DNA

The Mt-Haplogroup is H2a2a1

Let me know what you find.

Hinxton-4 has X-Matches with living people

October 22, 2014, 10:00 pm

≫ Next: Ancient DNA matches in FamilyTreeDNA

≪ Previous: Hinxton5 Ancient DNA Analysis

$

0

0

After batch processing for Hinxton-4 ancient DNA sample is complete in GEDMatch, I noticed it has matches with living people in X-Chromosome.

X-Matches

Taking a closer look at the first match with 500 SNPs / 5 cM with no errors, it is a solid match.

X-Match

Closer look at X

Interesting to see how ancient DNA matches living people. Hinxton-4 is said to be 2500-1800 years old. Can X-Chromosome segment with 500 SNPs / 5 cM match after 2000 years?

For a detailed analysis, please visit: Hinxton-4 DNA Analysis

---

Ancient DNA matches in FamilyTreeDNA

October 23, 2014, 12:47 pm

≫ Next: Ancient Hungarian Genome (NE5) Analysis

≪ Previous: Hinxton-4 has X-Matches with living people

$

0

0

FamilyTreeDNA has allowed to upload V3 files from 23andMe for free through their Autosomal Transfer. Meanwhile, I was genotyping ancient DNA samples from sequence reads uploaded by researchers. I also uploaded all files that has more SNPs than 23andMe V4 to GEDMatch. Interestingly, some ancient DNA samples like ClovisAnzick, LBK and Loschbour had matches with people living today in GEDMatch. I had blogged about this in the past month. Ancient DNA samples Altai Neanderthal, Clovis Anzick, Denisova, Hinxton-4, Linearbandkeramik, Loschbour and Palaeo Eskimo had significant V3 SNPs making it compatible with FamilyTreeDNA. I took advantage of the Autosomal Transfer and uploaded them. Out of all the uploads, 3 had matches.

Clovis Anzick

The genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana which is estimated by the authors as 12500 years old.

Matches for Clovis Anzick

Top Match for Clovis Anzick

I forgot to use the reference URL to unlock while uploading other kits, hence 41 more matches are still locked.

Linearbandkeramik

Genome sequence of a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany.

Matches for LBK

Top Match for LBK

I forgot to use the reference URL to unlock while uploading other kits, hence 3 more matches are still locked.

Loschbour

Genome sequence of a ~8,000 year old skeleton from the Loschbour rock shelter in Heffingen, Luxembourg

Matches for Loschbour

Top Match for Loschbour

What's next?

I had requested a Ancient DNA group project which gives an opportunity for existing admins and co-admins who are interested to manage the project and kits who match who are interested can join which helps to better understand the ancient world. I had blurred the matches because, these matches are not open to anyone in FamilyTreeDNA. Hence, to respect privacy, I had to hide it. I am eagerly waiting for this project to get approved which helps to bring all ancient DNA matches closer and analyze further.


FTDNA AutosomalTransfer Links:

If you have done 23andMe V3 chip test and want to transfer for free to FTDNA, please use the below links to transfer as this will help me unlock all the matches without cost for me.

• FTDNA AutosomalTransfer (unlocks Clovis Anzick)
• FTDNA AutosomalTransfer (unlocks Linearbandkeramik)
• FTDNA AutosomalTransfer (unlocks Loschbour)

Ancient Hungarian Genome (NE5) Analysis

October 26, 2014, 5:08 am

≫ Next: Ancient Hungarian genome (BR2) Y-DNA and mtDNA

≪ Previous: Ancient DNA matches in FamilyTreeDNA

$

0

0

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 NE5 from Kompolt-Kigyósér site in Hungary into formats familiar to genetic genealogists and made available here. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999927.

Admixture

MDLP Admixture Calculator

Eurogenes Admixture Calculator

Eye Color

Runs of Homozygosity

RoH reveals NE5's parent's are not related in his genealogical timeframe.

Telomere

Telomere length of 5.03934 suggests that he was a teenage boy when he died.

Telomere length of 5.04 suggesting a teenage boy. (Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Y-DNA

Y-Haplogroup is C-F3393

Y-STR Markers

• DYS572 = 10
• DYS434 = 10
• DYS472 = 8
• DYS638 = 11
• DYS425 = 9

CODIS Markers

• TPOX = 8,8

Mt-DNA

Mt-DNA Haplogroup is J1c. The authors had mentioned it as J1c1 in the paper. However, the mtDNA SNPs I got goes only till J1c (probably related to quality as I emit only high confidence SNPs).

Ancient Hungarian genome (BR2) Y-DNA and mtDNA

October 26, 2014, 1:14 pm

≫ Next: Ancient Hungarian Genome (NE7) Analysis

≪ Previous: Ancient Hungarian Genome (NE5) Analysis

$

0

0

I was able to peek into Y-DNA and mt-DNA of Ancient Hungarian genome - BR2 (SRR1186791) before the completion of the processing. Since it is processed with BAM Analysis Kit 1.5 which has upgraded lobSTR 3.0.2, it has more accurate Y-STR values as well.

Y-Haplogroup

The Y-Haplogroup is J-M67 (or J2a1b as per ISOGG tree). The authors has mentioned it as J2a1. However, it is also positive for M67 and

Y-STR Markers

Y-STR	VALUE
DYS393	12
DYS446	12
DYS640	9
DYS490	12
DYS572	10
DYS455	12
DYS522	11
DYS450	8
DYS531	11
DYS590	8
DYS568	11
DYS487	13
DYS19/DYS394	14
DYS391	10
DYS434	9
DYS437	14
DYS439	11
DYS389B.1	17
DYS442	16
DYS438	9
DYS495	14
DYS436	12
DYS641	10
DYS472	8
DYS565	11
DYS511	9
DYS492	12
DYS643	10
DYS533	11
DYS607	18
GATA-A10	15
DYS426	11
DYS444	13
DYS537	11
YCAIIa/b	21
DYS425	14
DYS395S1a/b	15
DYS460	9
DYS462	11
DYS494	10
DYS594	10
DYS445	12
DYS485	16
DYS556	12
DYS636	11
DYS406S1	11
DYS448.2	8
DYS459a/b	9
DYS464a/b/c/d	15

Y-Search kit is: CREKK.

Please note that Y-STR markers DYS464, DYS459, DYS395S1, YCA II are ignored as it is not possible to find which one is a/b/c/d.

Mt-Haplogroup

The mt-DNA is K1a1a

Download

The mt-DNA and Y-DNA data for BR2 is available for download here.

Ancient Hungarian Genome (NE7) Analysis

October 27, 2014, 2:19 am

≫ Next: Accuracy of the ages of ancient DNA samples

≪ Previous: Ancient Hungarian genome (BR2) Y-DNA and mtDNA

$

0

0

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 NE7 from Apc-Berekalja I. site in Hungary into formats familiar to genetic genealogists and made it available for download here. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999928.

Admixture

MDLP Admixture Calculator

Dodecad V3 Admixture Calculator

Eurogenes Admixture Calculator

Eye Color

Eye Color

HIrisPlex Report

PBlueEye	NA
PIntermediateEye	NA
PBrownEye	NA
Full_AUC_BlueEye	0.940398377
Full_AUC_IntermediateEye	0.743643077
Full_AUC_BrownEye	0.945280146
Numb_missingSNPs_Eye	2
Name_missingSNPs_Eye	rs16891982_C/rs12913832_T
AUC_Loss_BlueEye	0.325363303
AUC_Loss_IntermediateEye	0.158600074
AUC_Loss_BrownEye	0.334931231
PBlondHair	0.528412718
PBrownHair	0.3337846
PRedHair	0.004163469
PBlackHair	0.133639213
Full_AUC_BlondHair	0.810615722
Full_AUC_BrownHair	0.75106119
Full_AUC_RedHair	0.922711998
Full_AUC_BlackHair	0.848113996
Numb_missingSNPs_Hair	9
Name_missingSNPs_Hair	rs86insA_A / Y152OCH_A / rs28777_C / rs16891982_C / rs4959270_A / rs2402130_G / rs12913832_T / rs2378249_C / rs683_G
AUC_Loss_BlondHair	0.096772454
AUC_Loss_BrownHair	0.053516898
AUC_Loss_RedHair	0.024799569
AUC_Loss_BlackHair	0.096513017
PLightHair	NA
PDarkHair	NA
Full_AUC_HairShade	0.905443611
Numb_missingSNPs_HairShade	7
Name_missingSNPs_HairShade	rs28777_C /rs16891982_C / rs4959270_A / rs2402130_G / rs12913832_T /rs2378249_C/ rs683_G
AUC_Loss_HairShade	0.123102156

Refer: http://www.erasmusmc.nl/47743/3604975/HIris?lang=en

HIrisPlex does not reveal the eye color. However, the closest hair color I was able to find based on above values using the paper, 'The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA'.

Runs of Homozygosity

RoH reveals NE7's parent's are 3rd or 4th cousins.

Telomere

Telomere length of 5.723 suggests that he was a boy around 10 years old when he died.

Telomere length of 5.723 suggesting a teenage boy. (Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Y-DNA

Y-Haplogroup is I-L1228

Y-STR Markers

• DYS590 = 8
• DYS439 = 12

CODIS Markers

• D7S820 = 13,13

Mt-DNA

Mt-DNA Haplogroup is N1a.

Accuracy of the ages of ancient DNA samples

October 29, 2014, 5:49 am

≫ Next: Ancient Hungarian Iron age genome - IR1

≪ Previous: Ancient Hungarian Genome (NE7) Analysis

$

0

0

I was so keen to compare ancient DNA samples with living people. Interestingly, some ancient DNA do match living people. I had been asked several times regarding, how accurate are the ages of these ancient DNA samples.

Introduction

It is generally accepted that radiometric dating is reasonably accurate and the accuracy can be improved by using different elements half-life on the same sample. It is also generally accepted that radiocarbon dating in particular can be calibrated using dendrochronology, which provides a more accurate age. However, both methods has one fundamental assumption that radio active decay rate is always a constant.

In the year 2010, (just 4 years back) scientists discovered that radioactive decay rate is not a constant ¹. The authors concluded the following:

(Conclusion from Power spectrum analyses of nuclear decay rates1)

Then in 2011, a review of this experimental evidence does conclude the sun is indeed causing this radioactive decay rate variation ². Let's listen to the authors themselves.

(Abstract from Analysis of Experiments Exhibiting Time-Varying Nuclear Decay Rates: Systematic Effects or New Physics?2)

(Conclusion from Analysis of Experiments Exhibiting Time-Varying Nuclear Decay Rates: Systematic Effects or New Physics?2)

Then in 2012, there is additional experimental evidence for sun influencing nuclear decay rates³.

(Conclusion from Additional experimental evidence for a solar influence on nuclear decay rates3)

(Conclusion from Additional experimental evidence for a solar influence on nuclear decay rates3)

Again in 2013, more evidences emerge that sun is causing variations in nuclear decay rate.

(Abstract from Spectral content of 22Na/44Ti decay data: implications for a solar influence.4)

Then this year, in 2014,

(Abstract from Comparative study of beta-decay data for eight nuclides measured at the Physikalisch-Technische Bundesanstalt5)

It seems to me most researchers do agree that the nuclear decay rate does vary even to the order of 10^-3, whether it is solar or not, there are difference in opinions ⁶.

Conclusion

Radiometric dating is useful only when the core assumption of radioactive decay rate is constant. When this is proven to vary based on external influences, then there is no guarantee that the radiometric dating can provide any reasonable age estimates. If nuclear decay rate varies based on solar activity, so does all the estimated ages using radiometric dating , including these ancient DNA samples also varies. Hence, the ages of these ancient DNA samples are not accurate.

References

¹ Javorsek II, D., P. A. Sturrock, R. N. Lasenby, A. N. Lasenby, J. B. Buncher, E. Fischbach, J. T. Gruenwald et al. "Power spectrum analyses of nuclear decay rates."Astroparticle Physics 34, no. 3 (2010): 173-178.

² Jenkins, Jere H., Ephraim Fischbach, Peter A. Sturrock, and Daniel W. Mundy. "Analysis of Experiments Exhibiting Time-Varying Nuclear Decay Rates: Systematic Effects or New Physics?."arXiv preprint arXiv:1106.1678 (2011).

³ Jenkins, Jere H., Kevin R. Herminghuysen, Thomas E. Blue, Ephraim Fischbach, Daniel Javorsek II, Andrew C. Kauffman, Daniel W. Mundy, Peter A. Sturrock, and Joseph W. Talnagi. "Additional experimental evidence for a solar influence on nuclear decay rates."Astroparticle Physics 37 (2012): 81-88.

⁴ O’Keefe, Daniel, Brittany L. Morreale, Robert H. Lee, John B. Buncher, J. H. Jenkins, Ephraim Fischbach, T. Gruenwald, D. Javorsek II, and Peter A. Sturrock. "Spectral content of 22Na/44Ti decay data: implications for a solar influence."Astrophysics and Space Science 344, no. 2 (2013): 297-303.

⁵ Sturrock, P. A., E. Fischbach, D. Javorsek II, J. H. Jenkins, R. H. Lee, J. Nistor, and J. D. Scargle. "Comparative study of beta-decay data for eight nuclides measured at the Physikalisch-Technische Bundesanstalt."Astroparticle Physics 59 (2014): 47-58.

⁶ Kossert, Karsten, and Ole Nähle. "Disproof of solar influence on the decay rates of 90Sr/90Y."arXiv preprint arXiv:1407.2493 (2014).

Ancient Hungarian Iron age genome - IR1

October 30, 2014, 12:28 pm

≫ Next: Big-Y CSV → Y-SNPs → ISOGG Y-Tree

≪ Previous: Accuracy of the ages of ancient DNA samples

$

0

0

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 IR1 (830-980 cal BC) from Ludas-Varjú-dűlő 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 upload to GEDMatch as kit# F999929.

Admixture

Dodecad V3 Aadmixture Calculator

Eurogenes K15 Admixture Calculator

MDLP K23b Admixture Calculator

Eye Color

GEDmatch Eye Color Prediction

HIrisPlex Report

PBlueEye	0.916574821
PIntermediateEye	0.052848709
PBrownEye	0.03057647
Full_AUC_BlueEye	0.940398377
Full_AUC_IntermediateEye	0.743643077
Full_AUC_BrownEye	0.945280146
Numb_missingSNPs_Eye	4
Name_missingSNPs_Eye	rs16891982_C / rs12203592_T / rs12896399_T / rs1393350_T
AUC_Loss_BlueEye	0.022900905
AUC_Loss_IntermediateEye	0.05986763
AUC_Loss_BrownEye	0.018971968
PBlondHair	0.685846523
PBrownHair	0.227750162
PRedHair	0.026530882
PBlackHair	0.059872433
Full_AUC_BlondHair	0.810615722
Full_AUC_BrownHair	0.75106119
Full_AUC_RedHair	0.922711998
Full_AUC_BlackHair	0.848113996
Numb_missingSNPs_Hair	12
Name_missingSNPs_Hair	rs86insA_A / rs885479_T / rs1805008_T / rs1805006_A / Y152OCH_A / rs2228479_A / rs1110400_C / rs28777_C / rs16891982_C / rs12821256_G / rs12203592_T / rs683_G
AUC_Loss_BlondHair	0.095088236
AUC_Loss_BrownHair	0.091919902
AUC_Loss_RedHair	0.093115552
AUC_Loss_BlackHair	0.0337268
PLightHair	0.920294911
PDarkHair	0.079705089
Full_AUC_HairShade	0.905443611
Numb_missingSNPs_HairShade	10
Name_missingSNPs_HairShade	rs885479_T / rs1805008_T / rs1805006_A / rs2228479_A / rs1110400_C / rs28777_C / rs16891982_C / rs12821256_G / rs12203592_T / rs683_G
AUC_Loss_HairShade	0.052745236

Ref: http://www.erasmusmc.nl/47743/3604975/HIris?lang=en

Runs of Homozygosity

RoH reveals IR1's parents are not related in his genealogical timeframe.

Telomere

Telomere length of 7.5229 suggests IR1 could be a child within age of ~5 when died.

Telomere length of 7.5229 suggesting a child of age less than 5. (Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Y-DNA

Y-Haplogroup is N-M231

Y-STR Markers

• DYS472 = 8
• DYS643 = 10
• DYS533 = 11
• DYS537 = 11
• YCAIIa/b = 18
• DYS460 = 11

Mt-DNA

Mt-DNA Haplogroup is G2a1

One-to-Many Comparison

X-Matches on GEDmatch

IR1 has some matches with living people on X-Chromosome.

Big-Y CSV → Y-SNPs → ISOGG Y-Tree

October 30, 2014, 7:36 pm

≫ Next: Analysis of Hungarian Copper age genome - CO1

≪ Previous: Ancient Hungarian Iron age genome - IR1

$

0

0

A few days later after receiving my Big-Y results, I felt the need to download Y-SNPs and plot them on ISOGG Y-Tree in an easy way. FTDNA initially did not provide any download of SNPs. So, the easiest way is to get it directly from the webpage, as the data was readily displayed as a table is to use a browser add-on. So, I went ahead with a Google Chrome Browser and built an add-on called Big Y AddOn, with the ability to download SNPs, and plot on ISOGG Y-Tree and Morley Y-Tree.

I then realized, Y-SNPs are not specific to Big Y testers, but also for Geno 2.0 and other Y-DNA testers. So, I split the Big Y Add-On and created a new called called ISOGG Y-Tree AddOn for Google Chrome. Meanwhile, FTDNA provided a CSV download with contains the Y-SNPs. Hence, I felt the original Big-Y Add On is redundant and depreciated it. I placed a notice in Chrome WebStore and also moved the project to obsolete section. But still more people seems to download it even though the Big Y add-on is obsolete. Hence, after nearly 8 months of operation, I unpublished the Big-Y Add-on from the Chrome WebStore.

So, the obvious question to many is, how to get Y-SNPs from the Big-Y CSV download in-order to use the ISOGG Y-Tree Add-On. The simple answer is, use the Merge-Y tool. I had been responding in emails individually for people who email me. Hence, I thought of  post it as a blog. Briefly, the below steps explain how to add the Big-Y CSV download file to Merge-Y tool, export the Y-SNPs and how to use the Y-SNPs in ISOGG Y-Tree Add-On.

Step 1: Download the Big-Y CSV Download

Step 2: Download the Merge-Y tool. Open it and add the downloaded Big-Y CSV as Y-DNA file.

Step 3: Make sure the file is properly parsed and loaded.

Step 4: In Merge-Y, click File (menu) -> and Export SNPs.

Step 5: It will prompt you to save as a file, which can be opened in a notepad. Open it, as copy it (Ctrl+C) into clipboard.

 Step 6: Install the ISOGG Y-Tree Chrome Addon in your Chrome Browser. Go to extensions in Google Chrome Browser.

Step 7: Click Options for ISOGG Y-Tree Addon.

Step 8: Enter a name and paste the Y-SNPs (Ctrl+V) in Y-SNPs section. Then, click 'Save'.

Step 9: Now, go to ISOGG Y-Tree: www.isogg.org/tree/ISOGG_YDNATreeTrunk.html

Step 10: Enjoy.

If you found these steps useful, feel free to comment below.

---

Analysis of Hungarian Copper age genome - CO1

October 30, 2014, 10:16 pm

≫ Next: How the Hinxtons are related to each other?

≪ Previous: Big-Y CSV → Y-SNPs → ISOGG Y-Tree

$

0

0

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 CO1 from Apc-Berekalja I. 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 upload to GEDMatch as kit# F999930.

Admixture

Eurogenes Admixture Calculator

Dodecad V3 Admixture Calculator

MDLP K23b Admixture Calculator

Eye Color

The above is only based on 3 SNPs, so it may not be accurate.

Runs of Homozygosity

RoH reveals parents of CO1 are not related in their genealogical timeframe.

Telomere

Telomere length of 4.27076 suggests that CO1 is a teenager around the age of 17.

Telomere length of 4.27076 suggesting she is a teenager. (Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Mt-DNA

Mt-Haplogroup is identified as H.

Matches

CO1 matches with atleast 1 living person.

How the Hinxtons are related to each other?

October 31, 2014, 3:17 am

≫ Next: Analysis of Hungarian Neolithic KO1 genome

≪ Previous: Analysis of Hungarian Copper age genome - CO1

$

0

0

Using Interpretome, based on compound segments below is how the Hinxtons are related.

All Hinxtons

Based on the above tree, Hinxton-2 and Hinxton-5 are closely related. The ancestor of both is closely related to Hinxton-1 than Hinxton-3 and Hinxton-4.

Hinxtons (excluding Hinxton-2)

Hinxtons (excluding Hinxton-5)

Hinxtons (excluding Hinxton-2 & Hinxton-5)

Excluding Hinxton-2, Hnxton-5 and both reveals, Hinxton-1 is closely related to Hinxton-5 and Hinxton-3 is closely related to Hinxton-2. Hinxton-4 is the most distantly related.

Combining the above data, below is how they are truly related, showing pedigree collapse in the hinxton's family tree.

Based on Runs of Homozygosity, we know the following.

• Hinxton-2 parents are first cousins.
• Hinxton-3 parents are first or second cousins.
• Hinxton-5 parents are half siblings.

We know that Hinxton-2, Hinxton-3 and Hinxton-5 are all females, while Hinxton-1 and Hinxton-4 are males. Hinxton-2, Hinxton-3 and Hinxton-5 are not related to each other in genealogical timeframe.

Analysis of Hungarian Neolithic KO1 genome

November 1, 2014, 2:35 pm

≫ Next: Analysis of Hungarian Neolithic genome - NE6

≪ Previous: How the Hinxtons are related to each other?

$

0

0

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 KO1 from Tiszaszőlős-Domaháza 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 upload to GEDMatch as kit# F999931.

Admixture

Dodecad v3 Admixture Calculator

Eurogenes Admixture Calculator

MDLP K23b Admixture Calculator

Eye Color

Eye Color

Runs of Homozygosity

RoH reveals parents of KO1 are related as distant cousins like 6-8th cousins.

Telomere

Telomere length of 7.12063 suggests that KO1 is a child around than 5 years old .

Mt-DNA

Mt-Haplogroup is identified as R3.

Y-DNA

Y-DNA is identified as I-L68 (or I2).

Analysis of Hungarian Neolithic genome - NE6

November 2, 2014, 6:03 pm

≫ Next: Analysis of Hungarian Bronze Age genome - BR2

≪ Previous: Analysis of Hungarian Neolithic KO1 genome

$

0

0

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 NE6 from Apc-Berekalja I. 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 upload to GEDMatch as kit# F999932.

Admixture

Dodecad V3 Admixture Calculator

Eurogenes Admixture Calculator

MDLP Admixture Calculator

I added HarappaWorld admixture results as well because of the Asian component. I did not include Ethiohelix because the sample is not purely African (as it is the calculator's requirement)..

HarappaWorld Admixture Calculator

Eye Color

Eye Color

Runs of Homozygosity

RoH reveals parents of NE6 are related as distant cousins like 6th or 7th cousins.

Telomere

Telomere length of 1.16512 suggests that NE6 is in his old age.

Telomere length of 1.165 corresponding to age 80 (adapted from learn.genetics.utah.edu/content/chromosomes/telomeres/)

Mt-DNA

Mt-Haplogroup is identified as K1a3a3.

Y-DNA

Y-haplogroup is identified as C-P255.

Analysis of Hungarian Bronze Age genome - BR2

November 3, 2014, 11:41 am

≫ Next: Ancient sample BR2 matches living people

≪ Previous: Analysis of Hungarian Neolithic genome - NE6

$

0

0

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 BR2 from Ludas-Varjú-dűlő 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 upload to GEDMatch as kit# F999933.

Admixture

Dodecad v3 Admixture Calculator

Eurogenes Admixture Calculator

MDLP K32b Calculator

Eye Color

Eye Color

HIrisPlex Eye and Hair Colour Report

rs86insA_A	NA
rs11547464_A	0
rs885479_T	NA
rs1805008_T	0
rs1805005_T	0
rs1805006_A	0
rs1805007_T	0
rs1805009_C	0
Y152OCH_A	NA
rs2228479_A	0
rs1110400_C	0
rs28777_C	0
rs16891982_C	0
rs12821256_G	0
rs4959270_A	2
rs12203592_T	1
rs1042602_T	0
rs1800407_A	0
rs2402130_G	1
rs12913832_T	0
rs2378249_C	0
rs12896399_T	0
rs1393350_T	0
rs683_G	NA
PBlueEye	0.884178265
PIntermediateEye	0.082985421
PBrownEye	0.032836314
Full_AUC_BlueEye	0.940398377
Full_AUC_IntermediateEye	0.743643077
Full_AUC_BrownEye	0.945280146
Numb_missingSNPs_Eye	0
Name_missingSNPs_Eye
AUC_Loss_BlueEye	0
AUC_Loss_IntermediateEye	0
AUC_Loss_BrownEye	0
PBlondHair	0.338027494
PBrownHair	0.536075322
PRedHair	0.006602122
PBlackHair	0.119295062
Full_AUC_BlondHair	0.810615722
Full_AUC_BrownHair	0.75106119
Full_AUC_RedHair	0.922711998
Full_AUC_BlackHair	0.848113996
Numb_missingSNPs_Hair	4
Name_missingSNPs_Hair	rs86insA_A / rs885479_T / Y152OCH_A / rs683_G
AUC_Loss_BlondHair	0.005431842
AUC_Loss_BrownHair	0.002979272
AUC_Loss_RedHair	0.011863807
AUC_Loss_BlackHair	0.000183178
PLightHair	0.752924169
PDarkHair	0.247075831
Full_AUC_HairShade	0.905443611
Numb_missingSNPs_HairShade	2
Name_missingSNPs_HairShade	rs885479_T/rs683_G
AUC_Loss_HairShade	0.000300687

Ref: http://www.erasmusmc.nl/47743/3604975/HIris?lang=en

The Eye color is mostly blue as per HIrisPlex eye report.

For hair color, below is the closest hair color match I can get.

Runs of Homozygosity

RoH reveals parents of BR2 are not related in their genealogical timeframe.

Telomere

Telomere length of 1.16512 suggests that BR2 is in his old age ~ 80 years old.

Telomere length of 1.16512 suggesting an age of ~80 (adapted from learn.genetics.utah.edu/content/chromosomes/telomeres/)

Mt-DNA and Y-DNA

Mt-Haplogroup is identified as K1a1a and Y-DNA is J-M67 (or J2a1b). For detailed analysis on mt-DNA and Y-DNA, please refer - Ancient Hungarian genome (BR2) Y-DNA and mtDNA.