PDA

View Full Version : West-Med isles paper - Fernandes et. al - 2020



artemv
03-06-2020, 03:34 PM
Some time after the paper was published, we finally have the *.bam files online.

URL to the paper: https://www.nature.com/articles/s41559-020-1102-0
URL to the main topic on AG: https://anthrogenica.com/showthread.php?19763-Spread-of-Steppe-ancestry-to-the-Western-Mediterranean-(Fernandes-et-al-2020)

So, lets's start exploring. I will begin with Sardinian I samples:


ID
Location
Age
mtDNA
Y-reported
Y-actual


I15946
Sardinia, Anghelu Ruju
4052-3959 calBCE
T2c1d
I2a2a
I2-preM223-(Y3670??)


I16166
Sardinia, Sa Ucca de su Tintirriolu
2950-2600 BCE
J1c1
I
I(I2?)


I16170
Sardinia, Anghelu Ruju
1451-1301 calBCE
H3am
I2
I2-pre(?)L160


I14675
Sardinia, Serra Crabiles
2141-1976 calBCE
J2b1a+16311C!
I2a2a2a
I2-M223-PF692


I14676
Sardinia, Serra Crabiles
2199-2032 calBCE
J1c3j
I2a2a2a
I2-M223-PF692



The samples are not that high quality, but that's what we have.

I15946
He has both ancestral and derived calls on M223. He also has a derived call for Y3670 equivalent and no calls for all the SNP's between M223 and Y3670.
Looking at Y-tree we can expect that he might be Y3670 (like 2 more samples from the study also belong to this hg), but he has 4 ancestral calls at M223 level. Some of those calls might be because of deamination, but not all, and its unlikely for deamination to happen on the same level. And we have no mixed reads for M223 equivalents.
M223 level mutations:
L34 A->C 1 read
FGC3551 T->C 2 reads
L387.2 T->C 2 reads
L700 T->C 1 read
CTS7272 T->A 2 reads
CTS1616 G->T 2 reads
L705.1 G->T 3 reads
FGC3552 G->A 1 read
L706.1 G->A 3 reads
CTS7391 C->T 2 reads
CTS4149 C->A 1 read

Y3670 equivavalent:
S25360 G->T 2 reads

I16166
I(I2?)
Very small file. He has one positive and one negative call for I2 equivalents and ancestral results for most downstream lines, also negative for all the I1 SNPs where he has calls. I guess he is I2 and that ancestral result is an error.
He could be from a very deep dead out branch, but still there are some major I2 branches where he has no calls at all, so there is a chance he is from one of those branches.
CTS4039 G->A 1 read
FGC12073 C->A 1 read

I16170
Finally we have I-P37.2 from ancient Sardinia!
He has 4 calls for L160 equivalents:


CTS4506 T->G 1 read
CTS11229 A->G 2 reads
PF4101 A->G 1 read

CTS3404 C->T 3 reads

UPDATE:
I14675
https://www.yfull.com/tree/I-PF692/
He has the only derived read for PF692, 3 derived SNPs for the higher level.


PF692 level:
L1228 G->C 1 read

Y3670 level:
S9403 C->T 2 reads
Y6098 T->C 5 reads
CTS9515 T->C 2 reads

I14675
https://www.yfull.com/tree/I-PF692/
Has 3 derived SNPs for PF692 equivalents.

L1228 G->C 6 reads
M9771 C->T 2 reads
S24785 A->G 1 read