The puzzle of the early Corded Ware grave

In a recent paper and talk, archaeologist Kristian Kristiansen mentions a very early Corded Ware (CW) burial in Tiefbrunn, Germany; one of a few that contain a hammer-headed bone pin, like those found in Yamnaya and Catacomb graves on the steppe, particularly in the North Caucasus region.

Sr isotope ratios suggest that the older man was non-local, while the young man and the child may be locals. The skulls of all three individuals exhibited signs of severe trauma and they had probably suffered violent deaths.

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The grave goods consisted of only a flint blade and a hammer-headed bone pin, laid down beside the older male. Such pins are rare in the CW of Central Europe, but common in the Pontic Steppe region where they occur in a variety of forms until they disappear around 2600 BC [38].

All three individuals from this grave had their genomes sequenced as part of The Rise project and were labeled RISE434, RISE435 and RISE436. This is how they cluster in my Principal Component Analysis (PCA) of ancient West Eurasia.

As far as I can tell, based on the Sr isotope ratios from Sjögren K-G, Price TD, Kristiansen K 2016, RISE436 is the older man with the pin and RISE434 the young man (see here).

But if so, what is the likely non-local RISE436 doing as the most western of the Corded Ware samples sequenced to date? And why are the potentially local RISE434 and RISE435 so much more Yamnaya-like than him?

My interpretation of these results is that RISE436 was the descendant of a proto-Corded Ware male migrant from the steppe, and that his mother may have been of pre-Corded Ware farmer stock from Central or East-Central Europe. Note that this individual belongs to the Eastern European Y-chromosome haplogroup R1a, Western European (?) mitochondrial haplogroup U5b1c2, and on the plot above clusters almost exactly half-way between Yamnaya and early European farmers (Europe_EN and Europe_MN).

On the other hand, the young man and infant may derive from a more fully developed Corded Ware community in Central Europe, largely made up of second and third generation migrants from the steppe.

Any other ideas?

Citations...

Sjögren K-G, Price TD, Kristiansen K (2016) Diet and Mobility in the Corded Ware of Central Europe. PLoS ONE 11(5): e0155083. doi:10.1371/journal.pone.0155083

Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Higher caste, lighter skin

The Journal of Investigative Dermatology has a new paper on the pigmentation genetics of populations from the Middle Gangetic Plain in northern India. Its main finding is that upper caste Indians are generally lighter skinned than other Indians, particularly those from tribal groups.

This shouldn't be surprising to most people, but now we have a clearer idea of the genetics behind this phenomenon, including a new marker (SNP rs2470102) that helps to better explain skin pigmentation differences within South Asia.

Those of you wondering how the ancient samples likely to be relevant to the population history of South Asia stack up in terms of the alleles at rs2470102, check out the spreadsheet HERE. See anything interesting? I reckon I can; in terms of this one SNP, pre-Neolithic Western Europeans were potentially darker skinned than most modern-day Indians, because they're all homozygous for the G allele.

Our understanding of genetics of skin pigmentation has been largely skewed towards populations of European ancestry imparting much less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate the skin pigmentation variation in a cohort of 1167 individuals in Middle Gangetic Plain of Indian subcontinent. Our data confirms the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies and also reveals association for rs2470102 SNP. Our haplotype analyses further help us to delineate the haplotype distribution across the social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated SNPs explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated SNPs studied across 52 diverse populations of the Indian subcontinent, reveals wide presence of the derived alleles, albeit their frequencies vary across populations. Our results show that both of the polymorphisms (rs1426654 and rs2470102) play an important role in skin pigmentation diversity of South Asians.

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However, some tribes show exceptionally high frequency of rs1426654-A allele for example Gujjar (Jammu and Kashmir -1) and Meena (Rajasthan -0.91) (Supplementary Table S3 online). These tribes have been also known to be fair skinned (Joshua project, https://joshuaproject.net/). Interestingly, Brahmins belonging to higher castes in the social hierarchy of the caste system (Supplementary text online), irrespective of their geographical locations (North- Kashmiri Pandits, Pandits of Haryana, Brahmins of Uttar UPradesh), Havik (Karnataka, South) show similar frequencies of rs1426654-A variant (0.83–1) (Supplementary Table S3 online).

Mishra, Anshuman et al., Genotype-phenotype study of Middle Gangetic Plain in India reveals association of rs2470102 with skin pigmentation, Journal of Investigative Dermatology, article in press, DOI: http://dx.doi.org/10.1016/j.jid.2016.10.043

The Metal Age invader that never was #2

I just figured out how the Metal Age invader that never was came about. Take a look at this slide from an FTDNA presentation by Dr. Michael Hammer.

Hammer's taken the ADMIXTURE analysis from Lazaridis et al. 2013 and labeled the clusters according to what he thinks they represent. FTDNA then basically copied the analysis and the cluster labels for their "Ancient Origins" test.

But those clusters do not represent what Hammer thinks they do, in other words ancient populations like Western Hunter-Gatherers (WHG) or Ancient North Eurasians (ANE). Ancient ancestry proportions are listed in other parts of the Lazaridis et al. paper, like table S.14.10.

Moreover, Hammer appears to be under the impression that the Metal Age invader (that never was) came from Asia, and today it is the Kalasha people of the Hindu Kush who carry the highest ancestry proportion from this ancient population (that, of course, never actually was).

First of all, the Bronze Age Yamnaya pastoralists and related groups (i.e. the real Metal Age invaders) expanded both into Europe and Asia from the Pontic-Caspian Steppe. Obviously, the Pontic-Caspian Steppe is located in what is now known as Eastern Europe, not Asia.

Secondly, the Kalasha people carry about the same amount of Yamnaya-related ancestry as present-day Northern and Eastern Europeans, not three or four times as much, which, as per the figure above, is what Hammer seems to think.

Formal stats-based Yamnaya-related (or Steppe_EMBA) ancestry proportions for Europeans are listed in Haak et al. 2015 and for South Asians, including the Kalasha, in Lazaridis et al. 2016. See below.

See also...

Who's your (proto) daddy Western Europeans?

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

Early Indo-European migrations map

Wikipedia has a new animated gif of early Indo-European migrations (available at various resolutions here). It's pretty good overall, but very speculative and potentially erroneous in parts. For instance, my understanding is that the Vedic Aryans did not emerge from BMAC per se, as the map suggests, but rather from a post-BMAC phenomenon heavily influenced by steppe pastoralists. Hi-res ancient DNA from BMAC and post-BMAC sites should be able to resolve this issue.

As far as I know, BMAC remains were being tested at Harvard earlier this year, but the year is almost out, and nothing has been published. So either David Reich and co. are keeping the results for a new paper on the Indo-European homeland question, or they couldn't get any usable data from the samples. Keep in mind that only 30-40% of the ancient remains that are tested at Harvard are successfully genotyped. I can imagine that the success rate for samples from arid locations, like former BMAC sites in Turkmenistan, is even lower.

Update 31/12/2016: Commentator Tapatuevik Kaarmkyno points us to an article from earlier this year at NIH Record featuring this quote from David Reich:"We’ve sequenced more than 1,000 samples in our own lab — there’s not enough time to publish". That's probably why the second half of 2016 was so agonizingly slow. Next year should be awesome.

See also...

Maybe first direct hints of Yamnaya-related gene flow into South Central Asia

Do it right or don't do it at all

At least a couple of academic teams working on the population history of Europe need to read this PDF and take it to heart.

This article reviews scientific publications that have attempted to use genetic and genomic data in order to investigate European migrations between the fourth and ninth centuries. It considers early single-locus studies that used mtDNA and y-chromosome data. These studies were successful in formulating hypotheses concerning migration and heterogeneity, primarily between the Continent and the British Isles and Iceland, but could only examine a small portion of the entire genetic inheritance. The article continues with a presentation of more recent genome-wide studies. In particular, it evaluates the problems of using modern genomic data to understand past migratory processes, arguing that modern DNA is a problematic source for understanding population histories of the past fifteen hundred years and urges the sequencing and analysis of ancient DNA. It also presents some of the problems of re­search teams that did not include archaeologists and historians as integral participants in the planning, collection, and evaluation of data. It concludes with a brief outline of the authors’ current project that examines migration between Pannonia and Italy in the sixth century.

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This work is necessarily interdisciplinary, something notably lacking in the majority of genetic studies. The Ralph and Coop study, while highly rigorous at the level of the population genetic analysis, included no historians or archaeologists, and the only historical literature cited, presumably to »identify« the Hunnic contribution to European population, was a general history of Europe, [25] a survey of Slavic history, [26] and two articles in the New Cambridge Medieval History. [27] The Busby et al. study also included no historians or archaeologists on its team, and the only historical literature cited was a Penguin History of the World, Peter Heather’s survey of the Early Middle Ages, and a survey of Muslims in Italy. [28] Unlike these studies, designed and executed exclusively by geneticists who then look through a few general historical handbooks to try to find stories that might explain their data, historians and archaeologists are integrated from the start in our project.

Patrick J. Geary and Krishna Veeramah, Mapping European Population Movement through Genomic Research [PDF download], Medieval Worlds, No. 4, 201, 65-78

So how many of you really read the preprints at bioRxiv?

There's a new preprint at bioRxiv about the spread of the plague across much of Eurasia via the expansions of Early Bronze Age steppe pastoralists. It's been up for a few days now. Judging by the number of tweets on the preprint, a lot of people have read it. Or have they?

The manuscript contains a glaring error, a couple times over, in which the authors mix up the Afanasievo Culture with the Andronovo Culture. That's OK, this is why we have preprints and bioRxiv. I just found it somewhat amusing to see one lonely voice pointing this out under the rash of tweets recommending the paper.

Update 20/12/2016: A corrected version of the preprint has just been posted at bioRxiv. See here.

See also...

Mobile and then some

The Metal Age invader that never was

FTDNA has launched a new "Ancient Origins" analysis, and I've been asked a few times now what I think of the "Metal Age invader" component in this test. Essentially, I share the view of one of the commentators in the comments here.

FTDNA now models Europeans as a mix of hunter-gatherers (Loschbour, La Brana 1 and Motala), early European farmers (Stuttgart, Iceman, LBK) and so called "Metal Age invaders" which are based on Corded Ware and Yamnaya samples - so the latter is what we more typically call "steppe admixture". (Plus they add non-European admixture in case someone has it very evidently.) This model looks crude for our present-day standards, and their results look very different from what I've seen here in Davidski's analyses or in other ancient-DNA calculators on Gedmatch, as their inferred proportions of steppe admixture are much lower, about half of that inferred by others. And moreover to me it looks completely wrong that FTDNA suggests that I (1/4 Italian, strong southwest European component) have more Metal Age invader admixture than my fully East Prussian grandmother.

Indeed, any Early Bronze Age Steppe-inspired component should peak at 40-50% amongst Northern and Eastern Euros. This apparently doesn't. Why? No idea.

I know better than almost anyone else that there's no such thing as a perfect ancestry test, and FTDNA has every right to offer an experimental analysis to its clients, so let's leave it at that. But if you want to see what an ADMIXTURE test with a half-decent Yamnaya component looks like, then check out my attempt HERE. These are graphs from the linked blog entry showing inferred levels of Yamnaya-related ancestry proportions for Europeans and West Asians.

See also...

Massive migration from the steppe is a source for Indo-European languages in Europe (Haak et al. 2015 preprint).

Wolfgang Haak et al., Massive migration from the steppe is a source for Indo-European languages in Europe, bioRxiv, Posted February 10, 2015, doi: http://dx.doi.org/10.1101/013433

See also...

The Metal Age invader that never was #2

Who's your (proto) daddy Western Europeans?

Mobile and then some

Update 07/12/2018: Europe's ancient proto-cities may have been ravaged by the plague

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I've now read the new Valtuena et al. prerprint a couple of times, and even though the plague angle is interesting, what really sticks out for me is how incredibly mobile our steppe ancestors were.

It's been obvious for a while now that during the Early Bronze Age there was a massive expansion from the Pontic-Caspian Steppe in all directions, as far as the Atlantic shores in the west and the Altai region in the east. However, considering the phylogeny of Yersinia pestis genomes in Valtuena et al., it looks like the Yamnaya and/or closely related peoples also regularly roved across the entire length of the Eurasian Steppe.

The oldest and phylogenetically most basal sample of Yersinia pestis to date comes from an Afanasievo skeleton from the Altai region dated to 4836-4625 YBP. Hot on its heels, the next oldest is a sample derived from the Afanasievo strain, but from a Corded Ware skeleton from the East Baltic dated to 4571-4422 BP. The two burial sites are separated by something like 3,000 kilometers.

It's unlikely that Yersinia pestis spread from the Pontic-Caspian Steppe, say, with the Yamnaya, both to the Altai region and the East Baltic, because it hasn't yet been found in any of the Yamnaya remains. It's also generally accepted that Yersinia pestis is indeed from Asia. So it must have been picked up by migrants from the Pontic-Caspian Steppe somewhere in Asia, probably the Altai region, whose descendants then returned to Europe with the bug, and may have taken part in the Corded Ware expansion.

But of course it doesn't end there, because it appears that the descendants or close relatives of the Baltic Corded Ware people then moved back to Asia, because a sample of Yersinia pestis derived from the Corded Ware strain is found in an Andronovo skeleton from the Altai region dated to 3694-3575 BP. Note also that the genome-wide genetic structure of most of the Andronovo individuals sampled to date is Corded Ware-like, in fact more so than Yamnaya-like. In other words, ancient human DNA also shows a very close relationship between Andronovo and the older Corded Ware.

Why were these people roving around so much? I know they were pastoralists and that the Eurasian Steppe became progressively drier during the Bronze Age, so it may have been necessary to move wherever suitable pastures were available. But still, it seems rather ridiculous that they spent so much energy on long range intercontinental travel when, by all accounts, all they had were wagons pulled by oxen.

Citation...

Valtuena et al., The Stone Age Plague: 1000 years of Persistence in Eurasia, bioRxiv, Posted December 15, 2016. doi: https://doi.org/10.1101/094243

See also...

So how many of you really read the preprints at bioRxiv?

Bronze Age dope dealers

More on the stone age plague

Update 07/12/2018: Europe's ancient proto-cities may have been ravaged by the plague

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Good stuff at bioRxiv:

Abstract: Molecular signatures of Yersinia pestis were recently identified in prehistoric Eurasian individuals, thus suggesting Y. pestis might have caused some form of plague in humans prior to the first historically documented pandemic. Here, we present four new Y. pestis genomes from the European Late Neolithic and Bronze Age (LNBA) dating from 4,500 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in the Y. pestis phylogeny that appears to be extinct today. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread of Y. pestis during the LNBA: Y. pestis may have entered Europe from Central Eurasia during an expansion of steppe pastoralists, possibly persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in subsequent human population movements.

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The first indication of plague in Europe is found in the Baltic region and coincides with the time of the arrival of the steppe component (Allentoft et al., 2015). The two Late Neolithic Y. pestis genomes from the Baltic in this study were reconstructed from individuals associated with the Corded Ware Complex (Gyvakarai1 and KunilaII). The Baltic Y. pestis genomes are genetically derived from the strain that was found in the ‘Andronovo Complex’ from the Altai region [my note: I think they mean Afanasievo], suggesting that the disease might have spread with steppe pastoralists from Central Eurasia to Eastern and Central Europe during their massive range expansion. The younger Late Neolithic Y. pestis genomes from Southern Germany are genetically derived from the Baltic strains and are found in individuals associated with the Bell Beaker Complex. Previous analysis have shown that Bell Beaker individuals from Germany also carry ‘steppe ancestry (Allentoft et al., 2015; Haak et al., 2015). This suggests that Y. pestis may have been spread further southwestwards analogous to the human steppe component. The youngest of the LNBA Y. pestis genomes (RISE505), found also in the Altai region, descends from the Central European strains, and thus suggest a spread back into the eastern steppes.

Valtuena et al., The Stone Age Plague: 1000 years of Persistence in Eurasia, bioRxiv, Posted December 15, 2016. doi: https://doi.org/10.1101/094243

See also...

Plague germs may have facilitated Bronze Age expansions from the steppe

Mobile and then some

So how many of you really read the preprints at bioRxiv?

Middle Ages: rotten time to be a spotted horse

Scientific Reports has a new paper on the history of coat patterns in domesticated horses and the domestication process itself. Emphasis is mine:

Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.

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In addition, we discovered that tobiano spotting, which only occurs in domestic horses and had thus far only been detected after 1500 BC, was present in the Eneolithic/Copper Age (Kazakhstan, cal. 3654–3630 BC, and Germany, cal. 3368–3101 BC). Similar to chestnut and sabino spotting, the tobiano phenotype appears to arise shortly after domestication, which is assumed to have started approximately 4000–3500 BC in the Ponto-Caspian steppe region (modern day Kazakhstan and Ukraine) [17].

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Moreover, the detection of the tobiano phenotype in two Eneolithic domestic horses from distant regions has important implications regarding the origins of horse domestication [17] and their subsequent distribution. It also supports previous claims that the emergence of domestic horses in Central Europe at the end of the fourth millennium BC was facilitated by introduced horses from the Ponto-Caspian steppe [19].

Wutke, S. et al. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci. Rep. 6, 38548; doi: 10.1038/srep38548 (2016).

See also...

Sintashta and Scythian horses came from Hyperborea