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Wednesday, January 18, 2017

qpAdm tour of Europe: the Bronze Age invasion


Thirty nine modern-day and ancient test populations, fourteen outgroups, and only two rejected models (with perennial European outliers Chuvashs and Saami). Not a bad effort. It has to be meaningful.




Interestingly, the only Neolithic sample that I could find to make this work, after an exhaustive search, was I1495 from the Mathieson et al. 2016 dataset. This is an individual from the Hungarian Plain dated to 4490-4360 calBCE, belonging to the Late Neolithic Lengyel Culture of East Central Europe.

In other words, this person lived not too long before the massive Early Bronze Age expansions from the steppes by Yamnaya and other such pastoralist groups. So it's probably not a coincidence that he fits the bill, because the steppe folk would have probably ran into his close relatives, and absorbed many of them, as they fanned out west across the European continent.

Also worth noting is that only a few European populations show extra Caucasus Hunter-Gatherer (Caucasus_HG) admixture at levels significant enough, say, >5%, to suggest that they may have acquired it independently of the pastoralist incursions from the steppe. They're all from Southeastern Europe, and include Albanians, Greeks and three out of the four Italian groups.

It's an interesting question how they ended up with this extra dollop of Caucasus_HG, if they didn't get it from Yamnaya and/or related steppe peoples. One way to potentially test this is to look for temporally more proximate West Asian sources than Caucasus_HG, like, say, Armenia_EBA or Jordan_EBA, and see how they go.




Indeed, Armenia_EBA improves the statistical fits for all of the Southeastern Europeans. Jordan_EBA improves the statistical fits for the Sicilians.

To check my methodology, I also tested Germans and Poles with Armenia_EBA. These two North-Central European groups also show extra low level Caucasus_HG ancestry. However, their statistical fits are not improved by Armenia_EBA, which is not surprising considering their geography.

Therefore, it's plausible that the Southeastern Europeans do carry Caucasus or Armenian-related ancestry that arrived in their part of Europe independently of the pastoralist incursions from the steppe. Based on the available ancient DNA, this may have happened at any time between the Late Neolithic and the Medieval Period, and via multiple population movements. We'll need a lot more ancient DNA to work that out.

See also...

qpAdm tour of Europe: Mesolithic to Neolithic transition

Friday, January 13, 2017

qpAdm tour of Europe: Mesolithic to Neolithic transition


For a while now I've been trying to work out a way to model present-day Europeans with qpAdm as a mixture of Neolithic and Mesolithic populations. It hasn't been easy, because often what works for some Europeans doesn't work for others. But I've finally figured it out.

The trick is to account for Siberian, East Asian and Sub-Saharan ancestry, by including the Nganasan from Siberia, Onge from the Andaman Islands, and Yoruba from West Africa, respectively, as reference pops.

Below is the spreadsheet with the results and outgroups. Judging by the chisq and tail prob, most of the fits aren't spectacular, but as far as I can tell, they work.

Moreover, in the entire analysis not a single standard error reached 2%. Based on my experience with qpAdm, that's a remarkable thing for such a complex analysis, and I think it suggests that the reference populations are relevant.

Interestingly, while, as expected, the Nganasan-related admixture peaks in far Northern Europe, the Onge-related ancestry is, perhaps surprisingly, most pronounced in Southern Europe. Any ideas why? My thoughts on that here.




Update 014/01/2017: If you guys want to reproduce my analysis, but you don't have the same dataset, which is more than likely, you should be able to get very similar results using the full Human Origins dataset. Try these reference pops and outgroups.

pleft
Barcin_Neolithic
Caucasus_HG (Kotias)
Eastern_HG (Karelia_HG x2, Samara_HG)
Nganasan
Onge
Western_HG (Hungary_HG, Iberia_HG, Loschbour)
Yoruba (from the HGDP)

pright
AG3-MA1
Chukchi
Han
Karitiana
Kostenki14
Levant_Neolithic
Mbuti (Mbuti.DG x3 from Fu et al.)
Papuan
Satsurblia
Ust_Ishim
Villabruna

If you're seeing "infeasible", then remove the redundant reference population that might be causing problems, usually Yoruba or Nganasan, and run again.

If it's still not working, then maybe your dataset is just too different in some way, perhaps with not enough markers (there should be around 200K SNPs available for these runs).

See also...

qpAdm tour of Europe: the Bronze Age invasion

Wednesday, January 11, 2017

East and West Eurasians separated at least 45,000 years ago, but...


Finally, something interesting. Open access at Molecular Biology and Evolution:

A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.

...

In our model, K14 fits well as unadmixed (aside from archaic introgression), but MA1 receives, in addition to its archaic admixture, a component of eastern Eurasian ancestry. The latter gene flow explains the preliminary residual f4 (MA1, K14; Ami, Ust’-Ishim), which is of a similar form to several other relatively poorly fitting statistics from our initial graph, for example f 4 (MA1, K14; Ami, New Guinea) = 2.00 (fitted 0.08; Z = 2.68) and f 4 (MA1, Ust’-Ishim; Ami, New Guinea) = 1.73 (fitted 0.08; Z = 2.49). We added this admixture into our model with its best-fitting source position (near the root of the East Asian lineage) and mixture proportion (17.4% East Asian-related ancestry, 95% CI 7.7–27.4%).

...

We note that a recent study (Lazaridis et al., 2016) found a cline of MA1-relatedness among a large number of present-day eastern Eurasian populations and argued for admixture from west to east instead; while the present analysis supports the other direction, an important subject for future work will be to reconcile these results.

Mark Lipson and David Reich, Working model of the deep relationships of diverse modern human genetic lineages outside of Africa, Mol Biol Evol (2017), doi: 10.1093/molbev/msw293

Monday, January 9, 2017

Forager country


The findings in this new paper at the Journal of Archaeological Science might help to explain the unusually high levels of Mesolithic ancestry amongst present-day Northeast Europeans.

Abstract: Pottery was adopted by hunter-gatherers in the Eastern Baltic at the end of the 6th millennium cal BC. To examine the motivations for this cultural and technological shift, here we report the organic residue analysis of ceramic vessels from the earliest pottery horizon (Narva) in this region. A combined approach using GC-MS, GC-C-IRMS and bulk IRMS of residues absorbed into the ceramic and charred surface deposits was employed. The results show that despite variable preservation, Narva ceramic vessels were preferentially used for processing aquatic products. We argue that pottery was part of a new Late Mesolithic subsistence strategy which included more intensive exploitation of aquatic foods and may have had important implications, such as increased sedentism and population growth.

Oras et al., The adoption of pottery by north-east European hunter-gatherers: Evidence from lipid residue analysis, Journal of Archaeological Science, Volume 78, February 2017, Pages 112–119

Related stuff...

Recent studies of ancient genomes have revealed two large-scale prehistoric population movements into Europe after the initial settlement by modern humans: A first expansion from the Near East that brought agricultural practices, also known as the Neolithic revolution; and a second migration from the East that was seen in a genetic component related to the Yamnaya pastoralists of the Pontic Steppe, which appears in Central Europe in people of the Late Neolithic Corded Ware and has been present in Europeans since then in a decreasing North-East to South-West gradient. This migration has been proposed to be the source of the majority of today’s Indo-European languages within Europe.

In this paper we aim to show how these processes affected the Eastern Baltic region where the archeological record shows a drastically different picture than Central and Southern Europe. While agricultural subsistence strategies were commonplace in most of the latter by the Middle Neolithic, ceramic-producing hunter-gatherer cultures still persisted in the Eastern Baltic up until around 4000 BP and only adopted domesticated plants and animals at a late stage after which they disappeared into the widespread Corded Ware culture.

We present the results of ancient DNA analyses of 81 individuals from the territory of today’s Lithuania, Latvia and Estonia that span from the Mesolithic to Bronze Age. Through study of the uniparentally inherited mtDNA and Y-chromosome as well as positions across the entire genome that are informative about ancient ancestry we reveal the dynamics of prehistoric population continuity and change within this understudied region and how they are reflected in today’s Baltic populations.

Mittnik et al., A genetic perspective on population dynamics of the pre-historic Eastern Baltic region, EAA 2016 presentation, TH4-11 Abstract 06

Sunday, January 8, 2017

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.

...

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

Saturday, January 7, 2017

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.

...

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

Friday, January 6, 2017

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.



Thursday, December 29, 2016

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 an 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

Saturday, December 24, 2016

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.

...

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

Wednesday, December 21, 2016

The waiting game


By all accounts we'll soon be inundated with a smörgåsbord of new ancient samples. But let's be honest, this wait is a major pain in the proverbial.

If nothing happens before the middle of next month, someone here should check out the talk below by Daniel Bradley at the upcoming Plant and Animal Genome (PAG XXV) conference in San Diego. It seems like Bradley et al. from Trinity College, Dublin, have sequenced a whole bunch of ancient (Neolithic + Bronze Age?) genomes from Eastern Europe, and they'll be using them to look at the Indo-European homeland question.

From my past reading, I'd say the Dublin team members have a habit of overplaying somewhat the role of Caucasus Hunter-Gatherers (CHG) in the population history of Europe and South Asia, probably because they were the first to sequence CHG genomes, which is understandable. But I hope they don't fall into the trap of proclaiming CHG as the Indo-European genetic component without very solid evidence.

Abstract: Large longitudinal surveys of genomic diversity have uncovered two significant shifts in ancestry components in European samples. The first of these coincided with the onset of Neolithic culture and the second occurred in the third Millennium BC around the transition from the Late Neolithic to the Bronze Age. The scale of these changes imply massive population movements which may have coincided with the spread of new languages. However, whether genome change was universally associated with these cultural horizons is not yet known. This talk will present ancient genome data from southwest and eastern Europe, will contrast their patterns of longitudinal change and speculate about language origins.

Bradley, Daniel G., Ancient Human Genomes, Transitions, Farmers and Language at the Edge of Europe, PAG XXV talk, Number W258, San Diego, January 15, 2:42 PM.