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Tuesday, August 27, 2019

Isotopes vs ancient DNA in prehistoric Scandinavia

Four of the samples from the recent Frei et al. paper on human mobility in prehistoric southern Scandinavia are in my Global25 datasheets. Their genomes were published along with Allentoft et al. back in 2015. So I thought it might be interesting to check whether their strontium isotope ratios correlated with their genomic profiles.

In the Principal Component Analysis (PCA) below, RISE61 is a subtle outlier along the horizontal axis compared to the other three Nordic ancients, as well as a Danish individual representative of the present-day Danish gene pool. Also note that RISE61 shows the most unusual strontium isotope ratio (0.712588). The PCA was run with an online tool freely available here.

To help drive the point home, here's a figure from Frei et al., edited by me to show the positions of RISE47, RISE61 and RISE71. If RISE276 was also in this graph, he'd be sitting well under the "local" baseline, in roughly the same spot along the vertical axis as RISE47.

Interestingly, RISE61 belongs to Y-chromosome haplogroup R1a-M417, while RISE47 and RISE276, who appear to have been locals, both belong to R1b-M269. My guess is that RISE61 was a recent migrant from a more northerly part of Scandinavia dominated by the Battle-Axe culture (BAC). The BAC population was probably rich in R1a-M417 because it moved into Scandinavia from the Pontic-Caspian steppe via the East Baltic. This is what Frei et al. say about RISE61 and his burial site:

The double passage grave of Kyndeløse (Fig 1, S1 File) located on the island of Zealand yielded 70 individuals as well as a large number of grave goods, including flint artefacts, ceramics, and tooth and amber beads. We conducted strontium isotope analyses of seven individuals from Kyndeløse encompassing a period of c. 1000 years, indicating the prolonged use of this passage grave. The oldest of the seven individuals is a female (RISE 65) from whom we measured a “local” strontium isotope signature ( 87 Sr/ 86 Sr = 0.7099). Similar values were measured in five other individuals, including adult males and females. Only a single individual from Kyndeløse, an adult male (RISE 61) yielded a somewhat different strontium isotope signature of 87 Sr/ 86 Sr = 0.7126 which seems to indicate a non-local provenance. The skull of this male individual revealed healed porosities in the eye orbits, cribra orbitalia, a condition which is possibly linked to a vitamin deficiency during childhood, such as iron deficiency.

By the way, RISE47 was buried in a flat grave, which suggests that he was a commoner. RISE276 was found in a peat bog in Trundholm, where the famous Trundholm sun chariot was discovered (see here). He may have been a human sacrifice.


Frei KM, Bergerbrant S, Sjögren K-G, Jørkov ML, Lynnerup N, Harvig L, et al. (2019) Mapping human mobility during the third and second millennia BC in present-day Denmark. PLoS ONE 14(8): e0219850.

See also...

Commoner or elite?

Who were the people of the Nordic Bronze Age?

They came, they saw, and they mixed

Tuesday, August 20, 2019

Roopkund Lake dead

Fifteen of the Roopkund Lake samples from the Harney et al. paper published today at Nature Communications made it into the Global25 datasheets. Look for the prefix IND_Roopkund here...

Global25 datasheet ancient scaled

Global25 pop averages ancient scaled

Global25 datasheet ancient

Global25 pop averages ancient

Their genotypes are freely available in a ~590K SNP dataset via the Reich Lab here. I might be able to run more of the samples at some point if and when they're released in a dataset with more SNPs.

In any case, much like everyone else, I don't have a clue how those Mediterranean migrants ended up in the Himalayas back in the 1800s, but I do know where they came from. Most appear to have been from Crete, while others from mainland Greece. However, one of the individuals that I was able to analyze with the Global25 was almost certainly an Anatolian Greek. Below are a couple of Principal Component Analyses (PCA) based on the Global25 data. The relevant datasheet is available here.

I don't yet have a strong opinion about the origins of the earlier, typically South Asian Roopkund dead. They may have been visitors from all over India, or members of different castes from northern India. A PCA with six of these individuals can be seen here and the relevant datasheet gotten here. Any thoughts? Feel free to share them in the comments below.

Update 23/08/2019: A new ~1240K SNP genotype dataset with the Roopkund Lake samples is now available here. More markers means that I can produce more accurate PCA and run almost twice as many of the samples. I've updated all of the datasheets accordingly. The links are the same.

See also...

Getting the most out of the Global25

A surprising twist to the Shirenzigou nomads story

The Poltavka outlier

Saturday, August 17, 2019

A surprising twist to the Shirenzigou nomads story

Remember those potentially Afanasievo-derived and Tocharian-related Shirenzigou nomads from the Ning et al. paper? Well, in my opinion, they're probably neither. The genotypes and other data for these Iron Age individuals from the eastern Tian Shan are available here.

Below are a few successful and not so successful qpAdm mixture models for them. Note that I tried to use a wide range of relevant "right pops", but also retain a lot of markers, specifically to be able to discriminate between different types of steppe and steppe-derived sources of gene flow (refer to the full output). Admittedly, the Shirenzigou nomads can be modeled with Afanasievo-related ancestry, but...

KAZ_Botai 0.161±0.023
KAZ_Wusun 0.490±0.023
NPL_Mebrak_2125BP 0.349±0.019

chisq 5.793
tail prob 0.926172
Full output

KAZ_Botai 0.143±0.022
NPL_Mebrak_2125BP 0.295±0.019
Saka_Tian_Shan 0.562±0.024

chisq 6.796
tail prob 0.870794
Full output

KAZ_Botai 0.185±0.023
NPL_Mebrak_2125BP 0.428±0.021
RUS_Sintashta_MLBA 0.270±0.026
TJK_Sarazm_En 0.117±0.027

chisq 11.351
tail prob 0.414345
Full output

KAZ_Botai 0.032±0.027
KAZ_Zevakinskiy_LBA 0.567±0.025
NPL_Mebrak_2125BP 0.401±0.019

chisq 15.157
tail prob 0.232961
Full output

NPL_Mebrak_2125BP 0.452±0.031
RUS_Afanasievo 0.435±0.025
RUS_Okunevo_BA 0.114±0.049

chisq 19.808
tail prob 0.0708003
Full output

NPL_Mebrak_2125BP 0.409±0.031
RUS_Okunevo_BA 0.173±0.050
Yamnaya_RUS_Caucasus 0.418±0.026

chisq 20.453
tail prob 0.0589872
Full output

NPL_Mebrak_2125BP 0.464±0.033
RUS_Okunevo_BA 0.104±0.053
Yamnaya_RUS_Samara 0.432±0.027

chisq 27.189
tail prob 0.0072566
Full output

Both the Wusun and Saka are generally accepted to have been the speakers of Indo-Iranian languages. So it's possible that the Shirenzigou nomads were Indo-Iranian speakers too, or at least derived from such peoples.

Surprisingly, NPL_Mebrak_2125BP was the key to obtaining the best statistical fits. This is a trio of samples, roughly contemporaneous with the Shirenzigou nomads, from a burial site high up in the Himalayas in what is now Nepal (see here).

To be honest, I'm not quite sure why the Himalayan ancients work so well in my models. Perhaps they're just a really good proxy for an Iron Age population from the northern edge of the Tibetan Plateau?

By the way, most of the Shirenzigou nomads made it into the latest Global25 datasheets (see here). They can be analyzed in a variety of ways described in this blog post: Getting the most out of the Global25. Below is a screen cap of me comparing the effectiveness of Afanasievo, Sintashta and Wusun samples as proxies for the steppe ancestry in the Shirenzigou nomads with an online tool freely available here. As expected, the algorithm picks Sintashta ahead of Afanasievo, and the Wusun ahead of both.

See also...

They mixed up Huns with Tocharians

Some myths die hard

The mystery of the Sintashta people

Wednesday, August 14, 2019

Did South Caspian hunter-fishers really migrate to Eastern Europe?

The idea that most of the Near Eastern-related ancestry in the ancient populations of the Pontic-Caspian (PC) steppe is, one way or another, sourced from the territory of present-day Iran is a fairly popular one nowadays (for instance, see here). It might turn out to be correct, once there are enough relevant samples to test it properly, but in my opinion the chances of this are slim.

My skepticism is based on literally hours of analyses with the currently available ancients from the Caucaso-Caspian region, like, for instance, the admixture graphs below featuring foragers and early farmers from Russia, Georgia and Iran. The relevant qpGraph and dot files are available here.

Note that the further I move away from Eastern Europe in these graphs when looking for the source of the southern ancestry in the Eneolithic population from the southernmost part of the PC steppe (Piedmont_En), the more difficult it is for me to create a statistically sound model. What might this tell us about the provenance of this so called southern ancestry?

See also...

The PIE homeland controversy: August 2019 status report

Some myths die hard

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...