A Detailed Analysis of the Genetics of BE:

CC BY-NC-ND International by Open Genomes

Yaakov Kopel Likover was Y-DNA G-Y15861*, which is directly under G-Y12975.

G-Y1297 is probably the single most common Ashkenazi Y clade. The tMRCA is 1050 ybp, and so far, there seem to be no Sephardim in this clade.A tMRCA of 1050 ybp would just predate the settlment of Ashkenazi Jews in the Rhineland in the year 997 CE. The tMRCA of G-Y15861 is 850 ybp, which predates the documented settlement of Jews in Poland or Lithuania.

https://www.yfull.com/tree/G-Y15861/

The Ilumina 150 bp paired-end whole genome sequence produced excellent Y coverage, 99.85%L

The Y sequence produced 14 “best” or “acceptable” quality whole genome sequence SNPs, and one “ambiguous” quality SNP in a region with high homology.

https://www.yfull.com/branch-info/G-Y15861/

This yielded 11 SNPs that could be used for YFull’s branch age estimation. There were rather more SNPs for this sample than for the others in G-Y15861:

What is YFull's age estimation methodology?

The mtDNA haplogroup is T2b25, with an additional private SNP of G16129A:

https://haplogrep.i-med.ac.at/app/index.html

T2b25 appears to be European Neolithic in origin. It is found in Russia and England. There is however, one Ashkenazi match (without G16129A):

http://www.ianlogan.co.uk/sequences_by_group/t2b25-33_genbank_sequences.htm

Autosomal DNA ancestry analysis

The Harvard Reich Lab 1240k autosomal SNPs were extracted from the whole genome sequence. A Eurogenes Global25 principal components was obtained from David Wesolowski at Eurogenes.

http://eurogenes.blogspot.com/2019/07/getting-most-out-of-global25_12.html

Restricted nMonte3

This is the ancestral components is based on a Monte Carlo method analysis of its Eurogenes Global25 principal components compared to all Global25 samples.

The restricted nMonte, which is limited to components above a certain percentage, which helps eliminate the statisical problem of overfitting.

The hierarchical cluster analysis (clustered mean-constrained regularization) is a way to elimintate covariance between samples in different populations.)

Here is a technical explanation of nMonte3.

This is a Ward’s distance-squared clustering tree which

Eurogenes Global25 Ward's distance-squared tree using scaled data with 500 Ashkenazi Jews

http://open-genomes.org/analysis/PCA/nMonte/getNmonte.html?id=OG3-penalty-0-limit-0.4-only-Modern-exclude-Ashkenazi_Jew

http://open-genomes.org/analysis/PCA/nMonte/getNmonte.html?id=OG3-penalty-0-limit-0.4-only-Modern-exclude-Jewish

http://open-genomes.org/analysis/PCA/nMonte/getNmonte.html?id=OG3-penalty-0-limit-0.4-exclude-Modern

http://open-genomes.org/analysis/PCA/nMonte/getNmonte.html?id=OG3-penalty-0-limit-0.4-pre-Medieval

http://open-genomes.org/analysis/PCA/nMonte/getNmonte.html?id=OG3-penalty-0-limit-0.4-pre-Iron_Age

http://open-genomes.org/analysis/PCA/nMonte/getNmonte.html?id=OG3-penalty-0-limit-0.4-pre-Bronze_Age

http://open-genomes.org/analysis/PCA/nMonte/getNmonte.html?id=OG3-penalty-0-limit-0.4-pre-Chalcolithic

Boruch Elbaum’s Major Histocompatiblity Complex (MHC) Class I alleles (HLA-A, HLA-B, and HLA-C) are the most common haplotype combination among a large set of Ashkenazim:

This haplotype is HLA-A*26 - HLA-B*38 - HLA-C*12.

https://en.wikipedia.org/wiki/Human_leukocyte_antigen

HLA Nomeclature explained:

http://hla.alleles.org/nomenclature/naming.html

Boruch Elbaum’s HLA antitypes predicted by HLAScan:

http://open-genomes.org/genomes/personal/OG3/OG3_HLA.txt

=====================================================

HLAscan v5.0

Report created

2018. 7. 7. 15:4:3

========================================================

HLA gene : HLA-A

# of considered types : 3182

----------- HLA-Types -----------

[Type 1] 24:02:01:03 EX3_8.45652_100 EX2_8.36296_100 EX4_8.09783_100 EX5_6.53846_100

[Type 2] 26:01:01:01 EX3_6.92391_100 EX2_11.1_100 EX4_7.76812_100 EX5_4.89744_100

========================================================

HLA gene : HLA-B

# of considered types : 3958

----------- HLA-Types -----------

[Type 1] 38:01:01 EX3_44.8986_100 EX2_28.7815_100 EX4_35.9565_100 EX5_12.2393_100

[Type 2] 38:01:01 EX3_44.8986_100 EX2_28.7815_100 EX4_35.9565_100 EX5_12.2393_100

=====================================================

HLA gene : HLA-C

# of considered types : 2735

----------- HLA-Types -----------

[Type 1] 12:03:01:02 EX3_31.9493_100 EX2_43.9333_100 EX4_18.8116_100 EX5_16.95_100

[Type 2] 12:03:06 EX3_31.9348_100 EX2_43.9333_100 EX4_10.0072_50 EX5_16.95_100

=====================================================

https://www.ncbi.nlm.nih.gov/pubmed/10082430

http://www.allelefrequencies.net/hla6003a.asp?hla_locus1=&hla_locus2=B*&hla_locus3=&hla_locus4=&hla_locus5=&hla_locus6=&hla_locus7=&hla_locus8=&hla_population=&hla_country=&hla_dataset=&hla_region=&hla_ethnic=Jew&hla_study=&hla_order=order_3&hla_sample_size_pattern=equal&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_loci=

Ashkenazi Jews in the Allele Frequencies in Worldwide Populations database are underlined in red, below. The order of the haplotypes is from most frequent among Jews to less frequent.
These are the most common haplotypes among all “Jewish” populations (the site includes Chuetas from Majorca):