R1b-M269 in the Bronze Age Levant (?)

The new Harvard genotype dataset that I blogged about recently includes a couple of potentially very useful samples from the Levant dated to 1400-1100 BCE. Search for IDs I2062 and I1934 in the anno files here. They’re both from an archeological paper about a Late Middle Bronze Age (LMBA) burial site in what is now Israel that was published back in 2017 (here).
Surprisingly, individual I2062 is listed in the anno files as belonging to Y-haplogroup R1b1a1a2, which is also known as R1b-M269. The reason that this is a surprise to me is because R1b-M269 is closely associated with the Bronze Age expansions of pastoralists from the Pontic-Caspian steppe in Eastern Europe, and these expansions didn’t impact the Levant in any direct or significant way.
The Y-haplogroup assignment may or may not be correct. Sometimes the Y-haplogroups in these sorts of datasheets are indeed wrong. Unfortunately, as far as I know, the BAM file for I2062 isn’t available anywhere online, so I can’t check whether he does really belong to R1b-M269. But, intriguingly, his autosomes do show a subtle signal of Yamnaya-related ancestry from the Pontic-Caspian steppe that is missing in earlier ancients from the Levant.
To characterize his genome-wide ancestry, I first ran a series of unsupervised and supervised analyses with the Global25/nMonte3 method (using this datasheet). For the sake of simplicity, I narrowed things down to the mixture models below based on three reference populations each. Levant_ISR_C is made up of Chalcolithic samples from Israel. The identities of the other reference sets should be obvious to most readers. If confused, feel free to ask for more details in the comments below.

Levant_ISR_MLBA:I2062
Levant_ISR_C,66.8
IRN_Seh_Gabi_C,27
Yamnaya_RUS_Samara,6.2
[1] distance%=1.8905
Levant_ISR_MLBA:I2062
Levant_ISR_C,66.2
Kura-Araxes_ARM_Kaps,30.2
Yamnaya_RUS_Samara,3.6
[1] distance%=2.0856
Levant_ISR_MLBA:I2062
Levant_ISR_C,67.8
Kura-Araxes_RUS_Velikent,31.8
Yamnaya_RUS_Samara,0.4
[1] distance%=2.1738

To further confirm the reliability of my models, I tested them with the formal statistics-based qpAdm software. As far as I can tell, the output returned by qpAdm looks very solid across the board.

Levant_ISR_MLBA_I2062
IRN_Seh_Gabi_C 0.193±0.052
Levant_ISR_C 0.710±0.038
Yamnaya_RUS_Samara 0.098±0.026
chisq 9.304
tail prob 0.67676
Full output
Levant_ISR_MLBA_I2062
Kura-Araxes_ARM_Kaps 0.249±0.076
Levant_ISR_C 0.681±0.051
Yamnaya_RUS_Samara 0.071±0.035
chisq 11.101
tail prob 0.52032
Full output
Levant_ISR_MLBA_I2062
Levant_ISR_C 0.661±0.042
Kura-Araxes_RUS_Velikent 0.339±0.042
chisq 7.979
tail prob 0.844942
Full output

Admittedly, even though I2062 can be modeled with Yamnaya-related admixture, he doesn’t need to be. Indeed, his ratio of this type of ancestry varies signifcantly between the models, from around 10% to nothing. This appears to be dependent on the geography of the non-Levant and non-Yamnaya reference populations; the closer that they are to the Pontic-Caspian steppe, the smaller the ratio of Yamnaya-related ancestry in I2062. I’d describe this as an artifact of the isolation-by-distance phenomenon, and it totally makese sense, but it prevents me from confirming beyond any doubt that I2062 does harbor genome-wide steppe ancestry. Unfortunately, individual I1934 doesn’t have enough data to be analyzed with the same methods.
By the way, what’s the chance that I2062 is an awesome proxy for the earliest Jews? I reckon it’s pretty good, considering that Samaritans from Israel are his closest present-day population in terms of genome-wide affinity. Who wants to test this theory with the Global25? If I see some good stuff in the comments I’ll post it here in an update.
See also…
Downloadable genotypes of present-day and ancient DNA data
Early chariot riders of Transcaucasia came from…
R-V1636: Eneolithic steppe > Kura-Araxes?

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