Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India

[ombustman]

Well, the title is from the article and it's a bit misleading since the samples that trace back to the Mediterranean are from the 1800s but here we go.

Ok so I was comparing modern-day Cretans to ancient samples (Global25_PCA_pop_averages_scaled) and I saw this.

I was like how on earth a sample from India is closest to modern-day Cretans?

IND_Roopkund_B is still the closest if you mix it with modern-day samples


I saw the same Indian samples on my own distance calculation (I'm 3/8 Cretan)


So I started researching and came across this article:
https://www.nature.com/articles/s41467-019-11357-9
You can read the full article but I'll include the important bits here.

"Abstract
Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake and find that they cluster into three distinct groups. A group of 23 individuals has ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.

Introduction
Nestled deep in the Himalayan mountains at 5029 m above sea level, Roopkund Lake is a small body of water (~40 m in diameter) that is colloquially referred to as Skeleton Lake due to the remains of several hundred ancient humans scattered around its shores (Fig. 1). Little is known about the origin of these skeletons, as they have never been subjected to systematic anthropological or archaeological scrutiny, in part due to the disturbed nature of the site, which is frequently affected by rockslides, and which is often visited by local pilgrims and hikers who have manipulated the skeletons and removed many of the artifacts3. There have been multiple proposals to explain the origins of these skeletons. Local folklore describes a pilgrimage to the nearby shrine of the mountain goddess, Nanda Devi, undertaken by a king and queen and their many attendants, who—due to their inappropriate, celebratory behavior—were struck down by the wrath of Nanda Devi4. It has also been suggested that these are the remains of an army or group of merchants who were caught in a storm. Finally, it has been suggested that they were the victims of an epidemic.
To shed light on the origin of the skeletons of Roopkund, we analyzed their remains using a series of bioarcheological analyses, including ancient DNA, stable isotope dietary reconstruction, radiocarbon dating, and osteological analysis. We find that the Roopkund skeletons belong to three genetically distinct groups that were deposited during multiple events, separated in time by approximately 1000 years. These findings refute previous suggestions that the skeletons of Roopkund Lake were deposited in a single catastrophic event.


Results (important bits)
The report also identifies the presence of both very robust and tall individuals (outside the range of almost all South Asians), and more gracile individuals, and hypothesizes based on this the presence of at least two distinct groups of individuals, consistent with our genetic findings.

Roopkund skeletons form three genetically distinct groups
We find that the Roopkund individuals cluster into three distinct groups, which we will henceforth refer to as Roopkund_A, Roopkund_B, and Roopkund_C (Fig. 2a). Individuals in Roopkund_A (n = 23) fall along a genetic gradient that includes most present-day South Asians. However, they do not fall in a tight cluster along this gradient, suggesting that they do not comprise a single endogamous group, and instead derive from a diversity of groups. Individuals belonging to the Roopkund_B cluster (n = 14) do not fall along this gradient and instead fall near present-day West Eurasians, suggesting that Roopkund_B individuals possess West Eurasian-related ancestry.

Consistent with the PCA, Roopkund_A has ancestry most closely matching Indian groups; Roopkund_B has ancestry most closely matching Greek and Cretan groups; and Roopkund_C has ancestry most closely matching Southeast Asian groups.

To further understand the West Eurasian-related affinity in the Roopkund_B cluster, we projected all the Roopkund individuals onto a second PCA designed to distinguish between sub-components of West Eurasian-related ancestry13,14 (Fig. 2b). Individuals assigned to the Roopkund_A and Roopkund_C groups cluster towards the top right of the PCA plot, close to present-day groups with Iranian ancestry, consistent with where populations with South Asian or East Asian ancestry cluster when projected onto such a plot13. Individuals belonging to the Roopkund_B group cluster toward the center of the plot, close to present-day people from mainland Greece and Crete15. We observe consistent patterns using the automated clustering software ADMIXTURE16 (Fig. 2c) and in pairwise FST statistics (Fig. 2d, e, Supplementary Data 2). The visual evidence from the PCA suggests that two individuals from the Roopkund_B group might represent genetic outliers (Fig. 2b). However, symmetry f4-statistics show that the two apparent outliers (one of which has relatively low coverage) are statistically indistinguishable in ancestry from individuals of the main Roopkund_B cluster relative to diverse comparison populations (Supplementary Data 3), and so we lump all the Roopkund_B individuals together in what follows.

Skeletons at Roopkund Lake were deposited in multiple events
The discovery of multiple, genetically distinct groups among the skeletons of Roopkund Lake raises the question of whether these individuals died simultaneously or during separate events. We used Accelerator Mass Spectrometry (AMS) radiocarbon dating to determine the age of the remains. We find that the Roopkund_A and Roopkund_B groups are separated in time by ~1000 years, with the calibrated dates for individuals assigned to the Roopkund_A group ranging from the 7th–10th centuries CE, and the calibrated dates for individuals assigned to the Roopkund_B group ranging from the 17th–20th centuries CE. These results demonstrate that the skeletons of Roopkund Lake perished in at least two separate events. For Roopkund_A, we detect non-overlapping 95% confidence intervals (for example individual I6943 dates to 675–769 CE, while individual I6941 dates to 894–985 CE), suggesting that even these individuals may not have died simultaneously. In contrast, the calibrated dates obtained for 13 Roopkund_B individuals and the single Roopkund_C individual all have mutually overlapping 95% confidence intervals.

Genetic affinities of the Roopkund subgroups
We used qpWave to test whether Roopkund_B is consistent with forming a genetic clade with any present-day population (that is, whether it is possible to model the two populations as descending entirely from the same ancestral population with no mixture with other groups since their split). We selected 26 present-day populations for comparison, with particular emphasis on West Eurasian-related groups (we analyzed the West Eurasian-related groups Basque, Crete, Cypriot, Egyptian, English, Estonian, Finnish, French, Georgian, German, Greek, Hungarian, Italian_North, Italian_South, Norwegian, Spanish, Syrian, Ukrainian, and the non-West-Eurasian-related groups Brahmin_Tiwari, Chukchi, Han, Karitiana, Mala, Mbuti, Onge, and Papuan). We find that Roopkund_B is consistent with forming a genetic clade only with individuals from present-day Crete. These results by no means imply that the Roopkund_B individuals originated in the island of Crete itself, although they suggest that their recent ancestors or they themselves came from a nearby region.

Discussion
The genetically, temporally, and isotopically heterogeneous composition of the groups at Roopkund Lake was unanticipated from the context in which the skeletons were found. Radiocarbon dating reveals at least two key phases of deposition of human remains separated by around one thousand years and with significant heterogeneity in the dates for the earlier individuals indicating that they could not all have died in a single catastrophic event.

Combining multiple lines of evidence, we suggest a possible explanation for the origin of at least some of the Roopkund_A individuals. Roopkund Lake is not situated on any major trade route, but it is on a present-day pilgrimage route—the Nanda Devi Raj Jat pilgrimage which today occurs every 12 years. As part of the event, pilgrims gather for worship and celebration along the route. Reliable descriptions of the pilgrimage ritual do not appear until the late-19th century, but inscriptions in nearby temples dating to between the 8th and 10th centuries suggest potential earlier origins. We view the hypothesis of mass death during a pilgrimage event as a plausible explanation for at least some of the individuals in the Roopkund_A cluster.

The Roopkund_B cluster is more puzzling. It is tempting to hypothesize that the Roopkund_B individuals descend from Indo-Greek populations established after the time of Alexander the Great, who may have contributed ancestry to some present-day groups like the Kalash21. However, this is unlikely, as such a group would be expected to have admixture with groups with more typical South Asian ancestry (as the Kalash do), or would be expected to be inbred and to have relatively low genetic diversity. However, the Roopkund_B individuals have evidence for neither pattern. Combining different lines of evidence, the data suggest instead that what we have sampled is a group of unrelated men and women who were born in the eastern Mediterranean during the period of Ottoman political control. As suggested by their consumption of a predominantly terrestrial, rather than marine-based diet, they may have lived in an inland location, eventually traveling to and dying in the Himalayas. Whether they were participating in a pilgrimage or were drawn to Roopkund Lake for other reasons, is a mystery. It would be surprising for a Hindu pilgrimage to be practiced by a large group of travelers from the eastern Mediterranean where Hindu practices have not been common; Hindu practice at this time might be more plausible for a southeast Asian individual with an ancestry type like that seen in the Roopkund_C individual. Given that the Roopkund_B and Roopkund_C individuals died only in the last few centuries, an important direction for future investigation will be to carry out archival research to determine if there were reports of large foreign traveling parties dying in the region over the last few hundred years."

End of the article

I came across this comment under the same article which sounds plausible to me



Below are more articles about this subject:

Roopkund Lake dead
https://eurogenes.blogspot.com/2019/...lake-dead.html

The Fascinating Secrets of Roopkund Lake
https://wanderwisdom.com/travel-dest...l-of-Skeletons

[Miko]

Throughout all of the modern era, diverse Caucasoid populations went to other parts of the world and dominated them.

Some examples are the Sephardim in N. Africa, the Spanish in America, the Jesuits in Asia and seems that Greeks went to S. Asia.

[Petalpusher]

Just a Greek from the 1800 who came to work there as pointed out in the comments. Identical to modern greeks, and there s even one from the Roopkund_B whos autosomal profile is like N.Italian. It doesn't make sense even back from Alexander time as they would have been mixed with locals, or with trace of inbreeding in a small community which they didn't find.