March 16, 2018

Ancient DNA from the Balkans

This study has been for several months around but I have not discussed until now and is well worth a mention.

Ian Mathieson et al., The Genomic History Of Southeastern Europe. BioRXiv (pre-pub) 2017. doi:10.1101/135616

There is a lot of ancient autosomal DNA from the region but it basically says one thing: everything was almost exactly as expected from archaeology. The Karanovo-Gumelnita people, famed for inventing the Bronze Age a whole millenium earlier than anyone else, and nearby related cultures, were within the mainstream (Vasconic) Neolithic genetic grouping. This changed however with the kurgan invasion expressed primarily in the Ezero culture, which I've been told should be considered direct precursors of Thracians. But the change is not something radical: more genetic affinity with the steppe is visible than before and more generalized through all samples. 

Fig. 1-D - Supervised ADMIXTURE plot, modeling each ancient individual (one per row), as a mixture of
populations represented by clusters containing Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green).
  (click to expand)

Well, it is not exactly everything what is as expected, if we consider Polish Globular Amphorae culture, which I would have expected to be at least somewhat steppary, Indoeuropean, already but were not. Thus it seems I have to concede on this culture and its precursors being still part of the Vasconic Neolithic. This makes Indoeuropean penetration into Central-North Europe a much more sudden episode and one directly tied to Corded Ware culture and nothing else. It must have been perceived by its victims like a massive catastrophe, because it was a huge area which they conquered and to a large extent colonized in a very short span of time.

Lots of R1b in Epipaleolithic Balkans

Most interesting anyhow is the huge hoard of ancient Y-DNA R1b in the Iron Gates region (Lepenski Vir) before the Neolithic. This not only demonstrates, again, that this haplogroup is Paleoeuropean, at least in part, but, quite intriguingly makes earlier findings on modern data suggesting a possible origin or R1b-M269 in or near modern Serbia (Morelli 2010 and Myres 2010) at least somewhat plausible. However none of the Iron Gates R1b is described as R1b-M269 and in some cases it is excluded that it could be this sublineage. 

Thus the issue of the ultimate origins of this key lineage remains open, but let me underline that these Iron Gate individuals belonged to the WHG grouping, as did Villabruna (so far the oldest R1b carrier kown) and that they breach this way the assumed haplogroup homogeneity I2 conceived on merely Central and Northern European samples. Just as happened with mtDNA U haplogroup homogeneity when mtDNA H was detected by several independent studies of Iberian ancient DNA. It is normal to expect more diversity towards the south for several reasons but maybe the most critical of them is just average temperature, which makes the southern lands naturally more fertile (notably so for crops domesticated in the Middle East) and easier to inhabit. 

This trend was only broken in the Middle Ages when the heavy plough allowed the improved exploitation of deep Oceanic soils, being useless in the Mediterranean region of shallow soils however. It was only then when the center of European development moved from south to north, to Belgium specifically, where it remains till present day. So let's take Southern Europe a bit seriously, please.

Ancient genomes of SE Asia

Just a quick mention because I have such a long queue of stuff from Europe that I really have no time to look but very shallowly onto this study, which looks extremely interesting. Credit for the reference to Kristiina.

Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter et al., Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia, BioRXiv (pre-pub) 2018. doi:10.1101/278374


Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

March 2, 2018

Two big issues with Olalde 2018 (Indoeuropean Bell Beaker speculation)

"Just for being published in Nature it does not mean it is necessarily wrong" (popular saying).

Iñigo Olalde et al., The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe. doi:10.1101/135962 (pre-pub version, no way I'm spending 1/3 of my monthly income on this, in case you're willing to waste your money, it's been recently published in Nature)

Issue 1: All comparisons are made between Anatolia Neolithic or other Early Neolithic in some cases and Yamna or Corded Ware.  Late Neolithic is not used nor, critically, is Hunter-Gatherer populations or anything related. 

This means that everything will be much more Yamna-like than it should, just because Yamna are 50% HG, while Early Neolithic are very low in this component. 

This is very apparent in the PCA:

It's junk-in: junk-out.

Issue 2: there is a huge sampling gap precisely where ancient mtDNA (and modern Y-DNA) tells us that the origin of the modern West-Central European genetics should be: in France and nearby areas like the Basque Country, West Germany. Sure: they sample some Eastern French sites but see "issue 1" above.

Nuff said.

February 21, 2018

Caribbean Taino ancient DNA still alive in admixed populations

Taino Native Americans also had a very high genetic diversity, comparable to other continental large native populations such as Andeans or Amazonians, what speaks of high mobility in the Caribbean islands before European colonization.

The mitochondrial lineage B2 was sequenced, although it is today rare in the region.

Hannes Schroeder et al., Origins and genetic legacies of the Caribbean Taino. PNAS 2018. DOI:10.1073/pnas.1716839115

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Fig. 2.
Taino demography. Total estimated length of genomic ROH for the Taino and the Clovis genome (13) and selected Native American and Siberian genomes (15, 31, 32) in a series of length categories. ROH distributions for modern individuals have been condensed into population-level silhouettes (SI Appendix, section 14).

February 17, 2018

Ironworks the Iron Age style: the true thing done again by Burkinabe elders for the sake of historical document

This is a truly fascinating film, made by the people of Burkina Faso documenting their own, now vanishing tradition of iron smelting and forging, done again for the sake of historical documentation by the elders who used to do it decades ago (and some youngsters helping too) reproducing all the steps: from charcoal making and iron ore mining and selection, to the construction of the furnaces, the smelting of ore and finally tool-making itself. I cannot recommend it more wholeheartedly:

Obsidian exchange in Neolithic Sicily and Sardinia (video)

Thanks to Theasparagus for noticing this quite interesting video-lesson on quite obviously seagoing peoples of the Central Mediterranean and their journeys to distant volcanic islands to obtain the valuable obsidian (sharper than a scalpel) and also to the mainland to trade it for whatever goods.

February 14, 2018

Dystruct versus Admixture

Not really able yet to discern if this is an alternative way ahead for autosomal archaeogenetics or just another dead end. But it does seem interesting enough to mention here in any case.

It may be very important in the deciphering of the so-called "ANE" ghostly genetic influence.

Tyler A. Joseph & Itsik Pe'er. Inference of population structure from ancient DNA. bioRXiv 2018 (pre-pub). DOI:10.1101/261131

Methods for inferring population structure from genetic information traditionally assume samples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision of this paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference of shared ancestry from data that include ancient DNA. By explicitly modeling population history and genetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry from ancient and contemporary samples. Formally, we use a normal approximation of drift, which allows a novel, efficient algorithm for optimizing model parameters using stochastic variational inference. We show that Dystruct outperforms the state of the art when individuals are sampled over time, as is common in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of 92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual converse of presenting ancestral samples as mixtures of contemporary groups.

Still digesting this one but I do find very intriguing that they claim that Dystruct has much less time-entropy than ADMIXTURE (i.e. the relation between ancient and modern populations seems to be better identified) and that, using this method they get that the Samara (proto-Indoeuropean) population becomes much more clearly related to Kostenki-14 (a Gravettian hunter-gatherer from the Don area) and that the Paleo-Siberian "ANE" individuals form then their own distinct cluster with very limited impact in Europe (but much larger in parts of Asia (not labeled: South Asia?). This Kostenki-Samara "orange" component keeps influencing Western Indoeuropeans (Corded Ware, Unetice) but at markedly decreasing frequencies of "purity". 

However the first admixture of Corded Ware is not with earlier farmers (mostly "green") but with some sort of late "hunter-gatherer" population ("brown" or "maroon" component. Only after the backlash of Bell Beaker, which in Central Europe appears as a mix of Neolithic peoples, Indoeuropeans and maybe even more of that mysterious extra HG element, we see some "return of the farmers", which clearly persists in Unetice.

In general, modern Europeans are (fig.5a, not shown here) quite "greener" than Unetice and some populations (I'm guessing Sardinians and Basques, no labels provided) have zero "orange" (IE) component, which ranges (my visual estimate) between 9% and  27% otherwise.

Fig.5-b (click to expand): Ancestry estimates for 92 ancient samples. The three leftmost samples are the Pleistocene hunter-gatherers. In Dystruct, late Neolithic samples and beyond present as a mixture of hunter-gatherers, Yamnaya steppe herders,and early Neolithic samples, matching supported historical migrations of steppe herders into Eastern and Western Europe.

February 13, 2018

Scandinavian hunter-gatherers had double west-east origins

SHG origins' mystery solved? What about possible Norwegian "EHG-like" genetic influences into Atlantic Europe?

Torsten Günther, Helena Malmström, Emma Svensson, Ayça Omrak et al. Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. bioRXiv 2017 (pre-pub). DOI:10.1101/164400

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

Fig. 1:
Mesolithic samples and their genetic affinities – (A) Map of the Mesolithic European samples used in this study. The pie charts show the model-based [16,17] estimates of genetic ancestry for each SHG individual. The map also displays the ice sheet covering Scandinavia 10,000 BP (most credible (solid line) and maximum extend (dashed line) following [10]). Newly sequenced sites are shown in bold and italics, SF11 is excluded from this map due to its low coverage (0.1x). Additional European EHG and WHG individuals used in this study derive from sites outside this map (...)

Intriguingly, Swedish Epipaleolithic peoples (SHG) have the light skin variant in the gene SLC45A2, variant that is now uniformly spread through all Europe and accounts for 15% of the skin color variance in a key Cape Verde study and that was so far attributed solely (or almost solely) to Neolithic farmers (among which it was fixated and who had indeed a very large genetic impact in the European subcontinent). They also have the blue eyes allele, as Western Hunter-Gatherers did. However, if we are to follow, Günther's explanations in this video, the variance of looks in Epipaleolithic Scandinavia was greater than in present day. 


PS- Legend says that when my namesake Fray Luis de León returned to his classroom after five years imprisoned by the Inquisition, he began his class with these words: "As we were saying yesterday..."

Expect less lengthy articles because I really want to use this blog as open notebook, and not spend so much time following news and dissecting them thoroughly, so my style may become a bit more telegraphic. 

I also don't know for how long I will be able to continue blogging, as my personal economic situation is bad and worsening and you never know when police may come and arrest you for saying "fuck the king" or whatever other quite reasonable opinion. We live very troubled times and I'm personally quite bad at winning.

Also my apologies in advance if I fail to quickly approve comments. I usually check my email once per day or so but sometimes I just forget. Please, be patient if that happens: I only censor fascism, racism, sexism and homophobia (and those individuals who have managed to really get on my nerves, and they know who they are). Sadly I have to keep pre-moderating all comments, else the lonely troll will get away with his abuses.

February 4, 2017

The patrilineage R1b-DF27 in North Iberia

Just weeks ago a new study on Northern Iberian Y-DNA, focused specifically on R1b-DF27, was published. It covers Asturias, Cantabria, Basque Country and Aragon, finding greater diversity in the Basque Country and Cantabria and lower in Aragon and Asturias.

Patricia Villaescusa et al., Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain. FSI-Genetics 2017. Pay per viewLINK [doi:10.1016/j.fsigen.2016.12.013]


The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27. Our results reveal frequencies over 35% of DF27 haplogroup in the four North Iberian populations analyzed and high frequencies for its subhaplogroups. Considering the low frequency of DF27 and its sublineages in most populations outside of the Iberian Peninsula, this haplogroup seems to have geographical significance; thus, indicating a possible Iberian patrilineal origin of vestiges bearing this haplogroup. The dataset presented here contributes with new data to better understand the complex genetic variability of the Y chromosome in the Iberian Peninsula, that can be applied in Forensic Genetics.

The study, quite conveniently, differentiates between "native Basques" (those whose patrilineal ancestors lived in the Basque Country for at least the last three generations) and "resident Basques" (those whose recent patrilineal ancestors immigrated, mostly from NW Iberia).

R1b-DF27 is one of four major R1b sublineages in Western Europe and one of the three "brothers" that can be tracked to an origin somewhere in what is now Southern France, most likely, i.e. together they form part of R1b-S116. The fourth lineage would be, naturally, R1b-U106, "brother" of S116 and found typically around the North Sea. It is the one with the southernmost distribution, being very dominant in Iberia and among Basques. Probably it is also important in all the south of modern France but clear data is missing as of now.

Reconstructed spread of R1b to Western Europe and within it (dates objectively unknown so far, own work)

This is the key data table of the study, showing the frequency of the various sublineages of R1b-DF27 ("*" means "others", so "DF27", without asterisk, means "all DF27" and "DF27*" means instead "remaining DF27 after exclusion of the other mentioned subclades"):

Click to expand (frequencies are absolute, relative to whole sample)
It is also worth sticking this other graph, which shows (top right) the (SNP-based) true phylogeny of the haplogroup R1b-DF27 and, complementarily, the (somewhat messy) haplotype structure based on a limited number of short tandem repeats (STR), in which only Z220 appears clearly defined:

Click to expand

The study is very limited in its scope but it does show that there is a very high diversity for this lineage among Basques. This however does not necessarily indicate that Basques are the direct origin: much more data from the rest of Iberia and very especially from France is required before we can jump to any conclusion. Based on the limited data we have, I am of the opinion that the lineage did not originate in Iberia most likely but rather in what is now Southern France, migrating southwards via the two natural corridors: the Basque Country and Catalonia. 

Sadly enough we just do not have enough modern data, much less ancient one, in order to issue a definitive judgment on the matter. However the overall pattern of distribution of R1b-S116 strongly suggest a "Southern French" origin, not just for "Iberian" DF27 but also for the other two "brother" lineages: "Alpine" U152 and "North Atlantic" M529. 

The big question is how and when did this expansion took place. A "South French" origin was much easier to explain when the Paleolithic continuity model seemed reasonable, however recent ancient DNA findings strongly suggest that the Neolithic and Chalcolithic saw major population changes in much of Europe until stabilization was achieved -- exact patterns vary on specific regions: in some cases this does not happen until the Bronze Age, in others, like the Basque Country and quite possibly the Atlantic parts of France, it may have happened much earlier, even as soon as the early Neolithic. 

So my best recipe for an explanation is that we have to look very carefully at what happened in Western Europe, particularly towards the Atlantic Ocean in that "transitional" period, when not just large cultural phenomena like Dolmenic Megalithism or later also Bell Beaker manifested in quite expansive and dynamic manner but also a dearth of smaller cultures were the actual social or ethnic pieces making them possible. For example it is plausible that Michelsberg culture (originating in Lower Rhineland apparently and swiftly replacing the early Neolithic LBK culture in Germany, North France and nearby areas) could be involved in the expansion southwards of R1b-U106 and other traits of the modern genetic pools we observe. Another culture well worth taking a look at is the Artenac culture, which expanded from Dordogne towards the North up to Belgium soon after the Michelsberg/SOM era. Rather than one single and sudden expansion of a well defined population, it seems to me that we are before a jigsaw puzzle of several cultures and several chronologies, related maybe but not exactly the same.

See also:

Thanks once again to Jean Lohizun.