Ancient Y-DNA haplogroups

This page hosts analyses of ancient human Y-chromosomal haplogroup inference from next generation sequencing data, performed with software YLeaf v.2. For information on data and interpretation, refer to the manual at Erasmus MC Resources.

As a quick reference on data interpretation, please read papers on ancient DNA damage, such as Dabney, Meyer, and Pääbo (2013), for information of which derivative (and ancestral) SNP calls may be wrong.

dna-fragmentation-deamination
Fragmentation and deamination. (A) A likely cause of fragmentation in ancient DNA is depurination, in which theN-glycosyl bond between a sugar and an adenine or guanine residue is cleaved, resulting in an abasic site. The DNA strand is then fragmented through b elimination, leaving 30-aldehydic and 50-phosphate ends. (B) Deamination of cytosine to uracil is the major mechanism leading to miscoding lesions in ancient DNA. DNA polymerases will incorporate an A across from the U, and in turn a T across from the A, causing apparent G to A and C to T substitutions.

Ancient DNA

The following data is ordered chronologically, following the official date of the published papers. Most samples are tested for two options (labelled in the output spreadsheet):

  1. Option 20/90, to test standard quality.
    • Minimum number of reads for each base above on the quality threshold: 1
    • Minimum quality for each read: 20
    • Minimum percentage of a base result for acceptance: 90
  2. Option 0/10, to examine most SNP calls:
    • Minimum number of reads for each base above on the quality threshold: 1
    • Minimum quality for each read: 0
    • Minimum percentage of a base result for acceptance: 10

Ning et al. Cell (2019)

Proto-Tocharian samples from Shirenzigou, officially reported as of hg. R1b1a1b-M269.

Sample_name: M15-1
Hg: R1b2
Hg_marker: R-PH491/etc*(xY105682)
Total_reads: 3141489
Valid_markers: 4337
QC-score: 1.0
QC-1: 1.0
QC-2: 1.0
QC-3: 1.0
See full output.


Sample_name: M012
Hg: R1b2b
Hg_marker: R-BY14575*(xY32793,Y104457)
Total_reads: 2695398
Valid_markers: 3631
QC-score: 1.0
QC-1: 1.0
QC-2: 1.0
QC-3: 1.0
See full output.

Olalde et al. Nature (2019)

Proto-Lusitanian sample from Coimbra, reported as of hg. R1b-P297.

Sample_name: I7687_1240k
Hg: R1b1a1b
Hg_marker: R-CTS1415^^/etc*(xA561,A1243,CTS8234,Z222,PF6584,DF106,S798,BY451^^,A543,L1403,FGC11317,L277.1,CTS7556)
Total_reads: 121116
Valid_markers: 328
QC-score: 1.0
QC-1: 1.0
QC-2: 1.0
QC-3: 1.0

See full output.

Mathieson et al. Nature (2017, 2018)

Balkans Chalcolithic

Balkan outlier from Smyadovo. Officially reported as of hg. R.

Sample_name: I2181
Hg: NA
Hg_marker: NA
Total_reads: 146894
Valid_markers: 713
QC-score: 0.0
QC-1: 0.0
QC-2: 1.0
QC-3: 1.0
See full output.

Poor coverage. Positive up to CT, then R-P280 (C->G), R1b1a1-CTS9018 (C->T) R1b1a1b-PF6452 (G->A), with no possibility of contrasting if they are due to damage.

Also, negative for P~-PF5867 (G->A, ditto), and P~CTS10081 (C->A).

Ukraine_Eneolithic

Sample with steppe ancestry from Alexandria. Officially reported as of hg. R1a-M417. Amateurs have reported it as of hg. R1a-Z93 (Y95+, Y26+, L657-).

Sample_name: I6561
Hg: NA
Hg_marker: NA
Total_reads: 2043663
Valid_markers: 10718
QC-score: 0.0
QC-1: 0.0
QC-2: 1.0
QC-3: 1.0
See full output.

It has positive calls up to R1a1a1-M417, and also R1a1a1b~-F3044, R1a1a1b~-CTS9754, even R1a1a1b2~-AM01870, possibly then R1a1a1b2-Z93.

The other positives are C->T, including R1a1a1b2a~-F3568, and R1a1a1b2a1~AM00483.

In fact, R1a1a1b2a1~-AM00479 (G->T) is negative.

Mathieson et al. Nature (2015)

Yamnaya

Sample from Yamnaya at Lopatino II, Samara, officially reported as of hg. R1b-L23. Genetiker reported it as of hg. R1b-L23 (Y410+, L51-).

Sample_name: I2181
Hg: NA
Hg_marker: NA
Total_reads: 146894
Valid_markers: 713
QC-score: 0.0
QC-1: 0.0
QC-2: 1.0
QC-3: 1.0
See full output.

Positive up to R1b-M269. Negative for R1b1a1b1a-L51 (G->A). Negative for multiple SNPs at R1b-L151.

Samara_Eneolithic

Three samples from Khvalynsk II.

The chieftain, officially reported as of hg. R1b-L752. Amateurs had reported it as of hg. R1b-Pre-V88, hg. R1b-M73, hg. R1a-V1636.

Sample_name: I0122
Hg: R1b1a2
Hg_marker: R-BY15369/etc*(xBY15332,Y109041)
Total_reads: 1914224
Valid_markers: 7449
QC-score: 1.0
QC-1: 1.0
QC-2: 1.0
QC-3: 1.0
See full output.


The sample reported as of hg. R1a-M459. Amateurs have reported it to be of hg. R1a-YP1272

Sample_name: I0433
Hg: NA
Hg_marker: NA
Total_reads: 1396905
Valid_markers: 5074
QC-score: 0.0
QC-1: 0.0
QC-2: 1.0
QC-3: 1.0
See full output.

It has positive calls up to R1a1, but negative for R1a1a-M198 and R1a1b-YP1272.


The sample reported as of hg. Q1a:

Sample_name: I0434
Hg: Q1
Hg_marker: Q-F2676*(xF4930,L57)
Total_reads: 147970
Valid_markers: 490
QC-score: 1.0
QC-1: 1.0
QC-2: 1.0
QC-3: 1.0
See full output.

It has negative calls for Q1b-L57 (G->A), Q1b-CTS8328 (C->T), Q1b1-L55 (G->A), and Q1b1-L476 (G->A). Most likely Q1(xQ1b), i.e. Q1a-F1096.

Samara hunter-gatherer

Officially reported as of hg. R1b-L754. Amateurs have reported it to be of hg. R1b-M73.

Sample_name: I0124
Hg: NA
Hg_marker: NA
Total_reads: 1272057
Valid_markers: 5080
QC-score: 0.0
QC-1: 0.0
QC-2: 1.0
QC-3: 1.0
See full output.

It has positive calls up to R1b-P297.
Positive for two R1b-M73 SNPs: R1b1a1a-Y13872 (C->T) and R1b1a1a2-BY15591 (G->C), but negative for others.
Positive for two R1b-M269 SNPs: R1b1a1b-L777 (T->C) and R1b1a1b-PF6436 (C->T), but negative for others.