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. Citation... 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. https://doi.org/10.1371/journal.pone.0219850 See also... Commoner or elite? Who were the people of the Nordic Bronze Age? They came, they saw, and they mixed
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.
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 ancientTheir 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. 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. 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...
CHN_Shirenzigou_IA 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 CHN_Shirenzigou_IA 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 CHN_Shirenzigou_IA 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 CHN_Shirenzigou_IA 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 CHN_Shirenzigou_IA 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 CHN_Shirenzigou_IA 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 CHN_Shirenzigou_IA 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 outputBoth 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. 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? 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...
Friday, August 2, 2019
The PIE homeland controversy: August 2019 status report
Archeologist David Anthony has a new paper on the Indo-European homeland debate titled Archaeology, Genetics, and Language in the Steppes: A Comment on Bomhard. It's part of a series of articles dealing with Allan R. Bomhard's "Caucasian substrate hypothesis" in the latest edition of The Journal of Indo-European Studies. It's also available, without any restrictions, here. Any thoughts? Feel free to share them in the comments below. Admittedly, I found this part somewhat puzzling (emphasis is mine):
It was the faint trace of WHG, perhaps 3% of whole Yamnaya genomes, that identified this admixture as coming from Europe, not the Caucasus, according to Wang et al. (2018). Colleagues in David Reich’s lab commented that this small fraction of WHG ancestry could have come from many different geographic places and populations.I think that's highly optimistic. It really should be obvious by now thanks to archeological and ancient genomic data, including both uniparental and genome-wide variants, that the Yamnaya people were practically entirely derived from Eneolithic populations native to the Pontic-Caspian (PC) steppe. So, in all likelihood, this was also the source of their minor WHG ancestry. Indeed, they clearly weren't some mishmash of geographically, culturally and genetically disparate groups that had just arrived in Eastern Europe, but the direct descendants of closely related and already significantly Yamnaya-like peoples associated with long-standing PC steppe archeological cultures such as Khvalynsk and Sredny Stog. I discussed this earlier this year, soon after the Wang et al. paper was published:
On Maykop ancestry in YamnayaI hope I'm wrong, but I get the feeling that the scientists at the Reich Lab are finding this difficult to accept, because it doesn't gel with their theory that archaic Proto-Indo-European (PIE) wasn't spoken on the PC steppe, but rather south of the Caucasus, and that late or rather nuclear PIE was introduced into the PC steppe by migrants from the Maykop culture who were somehow involved in the formation of the Yamnaya horizon. Inexplicably, after citing Wang et al. on multiple occasions and arguing against any significant gene flow between Maykop and Yamnaya groups, Anthony fails to mention Steppe Maykop. But the Steppe Maykop people are an awesome argument against the idea that there was anything more than occasional mating between the Maykop and Yamnaya populations, because they were wedged between them, and yet clearly distinct from both, with a surprisingly high ratio of West Siberian forager-related ancestry (see here and here).
Yamnaya_RUS_Caucasus RUS_Progress_En_PG2001 0.808±0.058 RUS_Steppe_Maykop 0.000 UKR_Sredny_Stog_II_En_I6561 0.192±0.058 chisq 13.859 tail prob 0.383882 Full outputYep, total population replacement with no significant gene flow between the two groups. Apparently, as far as I can tell, there's not even a hint that a few Steppe Maykop stragglers were incorporated into the ranks of the newcomers. Where did they go? Hard to say for now. Maybe they ran for the hills nearby? Intriguingly, Anthony reveals a few details about new samples from three different Eneolithic steppe burial sites associated with the Khvalynsk culture:
The Reich lab now has whole-genome aDNA data from more than 30 individuals from three Eneolithic cemeteries in the Volga steppes between the cities of Saratov and Samara (Khlopkov Bugor, Khvalynsk, and Ekaterinovka), all dated around the middle of the fifth millennium BC. ... Most of the males belonged to Y-chromosome haplogroup R1b1a, like almost all Yamnaya males, but Khvalynsk also had some minority Y-chromosome haplogroups (R1a, Q1a, J, I2a2) that do not appear or appear only rarely (I2a2) in Yamnaya graves.As far as I can tell, he suggests that they'll be published in the forthcoming Narasimhan et al. paper. If so, it sounds like the paper will have many more ancient samples than its early preprint that was posted at bioRxiv last year. For me the really fascinating thing in regards to these new samples is how scarce Y-haplogroup R1a appears to have been everywhere before the expansion by the putative Indo-European-speaking steppe ancestors of the Corded Ware culture (CWC) people. It's basically always outnumbered by other haplogroups wherever it's found prior to about 3,000 BCE, even on the PC steppe. But then, suddenly, its R1a-M417 subclade goes BOOM! And that's why I call it...
The beast among Y-haplogroupsAt this stage, I'm not sure how to interpret the presence of Y-haplogroup J in the Khvalynsk population. It may or may not be important to the PIE homeland debate. Keep in mind that J is present in two foragers from Karelia and Popovo, northern Russia, dated to the Mesolithic period and with no obvious foreign ancestry. So it need not have arrived north of the Caspian as late as the Eneolithic with migrants rich in southern ancestry from the Caucasus or what is now Iran. In other words, for the time being, the steppe PIE homeland theory appears safe. Update 20/12/2019: A note on Steppe Maykop See also... Is Yamnaya overrated? The PIE homeland controversy: January 2019 status report Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...