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Ironworks the Iron Age style: the true thing done again by Burkinabe elders for the sake of historical document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

January 9, 2017

Extensive ancient Iberian mtDNA analysis

A very interesting thesis on Iberian ancient mitochondrial DNA is available (found via Bell Beaker Blogger):

Christina Roth, Once upon a time in the West : paleogenetic analyses on Mesolithic to Early Bronze Age individuals from the Iberian Peninsula. University of Mainz (thesis), 2016. Freely availableLINK

As all theses, it is very extensive, and I can only make some comments here (space and time are always too limited, you know), hoping to grasp the most interesting aspects of it.

First of all Roth finds that Iberian hunter-gatherers (HGW in the paper) were not quite like Central European ones (HGC), at least not in the mtDNA. Instead, in this aspect the Central European hunter-gatherers were closer to Eastern European ones (HGE), as well as to the Pitted Ware late subneolithic population of Gotland.

Iberia-only mtDNA analysis

This will be a recurrent issue along the analysis she makes. But let's focus on Iberia by the moment. Notice that she does not just use her own data but also from many other sources, including some unpublished materials, this makes a bit difficult to follow all the details, so I feel I can only focus on the statistical analysis she makes and which is the core of the thesis.

Annotated by me, because I found the abbreviations quite hard to follow

The general overview is confirmed, with minor variations, in the cluster analysis (which I also took the liberty of annotating, but take my notes for what they are: mere scribbling on the margin in an attempt to better understand the data, nothing else):

Particular care not to take the arrows of my notes too seriously: they are just conceptual, a very loose sequencing of the available data for a very tentative visualization of it. If it helps you, cool, else ignore please.

In any case, it seems clear cluster 2 is more influenced by hunter-gatherer genetics and that, with the data available in this study, we reach the end of the timeline within it in the following regions: Upper Ebro and Basque Country (data up to Late Neolithic but see my own 2013 compilation for a longer period), Southern Iberia (up to Chalcolithic) Southeast and Northeast, this one after originally being in the "more Neolithic" cluster 1 (in fact the author does argue for Catalonia as main "gate" for Neolithic genetics into Iberia on light of the available data, which does not include another important "gate", the SE one, for lack of data for the early period).

Inversely, cluster 1 is more influenced by "farmer" genetics, first detected in the Northeast (Catalonia and nearby areas of Aragon) but then also affecting the Northern Plateau and the West (Central Portugal). This last is very important because it is here where a key civilizational hub, the oldest known civilization of the Atlantic shores, emerged in the Chalcolithic, playing a key role in the wider Megalithic and Bell Beaker phenomena. I have at times speculated that it might be the origin of "modernity" in Western European genetic pools but on light of this data I have to recant, the origin should be elsewhere, probably in/around what is now France (and therefore it's not likely to be directly related to Bell Beaker, except maybe in the islands, but rather to Michelsberg/SOM, Artenacian and such -- always in wait of more data, just a cautious hypothesis). 

Finally the farmer-leaning cluster reaches the Southern Plateau, near Madrid, what suggests a N→S move of the then-forming Cogotas I herder culture, rather than the opposite. 

What we do see is not inconsistent with modern Iberian genetics anyhow: while Central Europe seem to have seen an increase of "hunter-gatherer" genetics along time, in Iberia the main tendency is the opposite: an increase of "farmer" genetics and further dilution of the aboriginal genetic pool. There is however at least one clear exception in the Northeast and that is also consistent with modern Iberian genetics. Some regions (south, southeast and the totally unknown northwest) have only fragmentary sequences here, so unclear, although the final tendency, up to the Bronze Age, is to cluster 2b (i.e. mixed but rather tending to "hunter-gatherer" genetics).

To finish with the Iberia-only bloc, notice that these are the lineages found among early Iberian farmers by region (in color those haplogroups associated to the arrival of Neolithic per the available data):

Notice how the pool in the Northern region is quite modern-like, not yet exactly as it is locally today but it would pass quite unnoticed in a map of Europe.

Iberia and the rest of Europe

What about the pan-European context (with the usual huge blanks in France, Britain, etc.)? Quite interesting as well:

Annotated by Maju on fig. 23 (click to enlarge)

As mentioned before, the Iberian hunter gatherers (HGW) appear clearly distinct from their Central and Eastern cousins in the mtDNA analysis. And with all this Iberian dataset it becomes apparent that there seem to be two "zones of admixture": one for Iberians and another for Central Europeans, the difference being on which aborigines they mix with. 

Notice that it is not possible to differentiate here between local Central European and intrusive Eastern European admixture, as both aboriginal hunter-gatherer populations appear closely related in all analyses (maybe an artifact of the sampling strategy or maybe actually relevant, can't say). 

It also caught my eye that a German site (Blätterhöhle, Westfalia, famed because farmer and hunter-gatherers living side by side were located there some years ago), clusters intensely with Iberian hunter-gatherers and related populations. I have to research more on this matter (which I had ignored so far) but I suspect it may be very relevant, because we could get an even longer chain of early "modern" mtDNA pools, adding this site to Paternabidea (Navarre) and Gurgy (Burgundy), spanning a long stretch of Western Europe, an area quite neglected by archaeogenetics so far, it must be said.

It is also worth mentioning that UC (which I believe stands for Unetice Culture) pulls the "Central European zone of admixture" in the PCA downwards, with a polarity of its own, a polarity that should probably be considered as specifically Indoeuropean. 

The cluster analysis confirms much of what I just said above, not annotated for a change:

We see very clearly here a larger cluster more influenced by "farmer" genetics and a smaller one that includes all pre-Neolithic aborigines, plus two populations already post-Neolithic but clearly identifiable as at least largely aboriginal (PWC and BLA), plus a subcluster of Neolithic Iberians, from the North (NSE and EVN) and the West (CPE). 

The author notices that: Bernburg (BEC) and Funnel Beaker (FBC) samples (...) show almost no significant differences to any Iberian group, except to the Early Neolithic of Northern Spain (NSE) and Chalcolithic of East Spain (ESC). Hard to interpret but worth noticing, no doubt.

And there is a lot more in the thesis but I can only review so much, so take a look and tell me and the World if I'm missing something of relevance or you feel I'm misinterpreting something or whatever.

January 1, 2017

Chad's Eurasian genetic input similar to that in Ethiopia


Marc Haber et al. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations. AJHG 2016. Open accessLINK [doi:10.1016/j.ajhg.2016.10.012]


Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

Worth a read no doubt but careful, careful, careful with their chronological guesstimates. Their starting point is the assumption (once and again demonstrated all kinds of WRONG) of:

Eurasians and Africans diverged around 60,000–80,000 ya and subsequently had different patterns of population-size changes: in particular, compared with Africans, the Eurasian population experienced a sharp decrease in size ∼60,000 ya.

So add around 65-70% (x1.7) to all dates, else you are bound to fall in the pit of molecular-clock-o-logical self-complacent pseudoscience. So where it reads c. 6-7 Ka for the first migration (R1b-related), it should be 10,000 years ago (which is the actual dating of Afroasiatic expansion by most accounts, with origin not exactly in "Eurasia" but rather in or near Sudan, where those Eurasian lineages, R1b and J1, had since long before most likely), and when they say 3 Ka ago, it's probably 5000 years ago, within the context of Neolithic inflows possibly: 3000 years ago was already well into Ancient Egypt and peoples just did not cross it without proper paperwork anymore, actually 3000 years ago is the Bronze Age collapse and Egypt, Lower Egypt specifically, fell to Africans, to Libyans and other Berbers known as Meshwesh (Amazigh, probably from modern Tunisia) to be precise.

Dr. Haber: time to update your clock, it just doesn't work, and you are confusing people to no avail.

Forests burnt in Ice Age Europe


Jed O. Kaplan et al., Large Scale Anthropogenic Reduction of Forest Cover in Last Glacial Maximum Europe. PLoS ONE 2016. Open accessLINK [doi:10.1371/journal.pone.0166726]


Reconstructions of the vegetation of Europe during the Last Glacial Maximum (LGM) are an enigma. Pollen-based analyses have suggested that Europe was largely covered by steppe and tundra, and forests persisted only in small refugia. Climate-vegetation model simulations on the other hand have consistently suggested that broad areas of Europe would have been suitable for forest, even in the depths of the last glaciation. Here we reconcile models with data by demonstrating that the highly mobile groups of hunter-gatherers that inhabited Europe at the LGM could have substantially reduced forest cover through the ignition of wildfires. Similar to hunter-gatherers of the more recent past, Upper Paleolithic humans were masters of the use of fire, and preferred inhabiting semi-open landscapes to facilitate foraging, hunting and travel. Incorporating human agency into a dynamic vegetation-fire model and simulating forest cover shows that even small increases in wildfire frequency over natural background levels resulted in large changes in the forested area of Europe, in part because trees were already stressed by low atmospheric CO2 concentrations and the cold, dry, and highly variable climate. Our results suggest that the impact of humans on the glacial landscape of Europe may be one of the earliest large-scale anthropogenic modifications of the earth system.

Not sure what to think, really. In any case the data they manage and share with us is very much worth taking a look at.

Reconstructing Sardinian population history

A very interesting pre-pub study, dealing with Sardinian genetics in great sub-national detail but also within the wider European and Mediterranean context, became available in the last weeks. I won't probably be able to make justice to it here, so please take a look yourselves.

Charleston W.K. Chiang et al., Population history of the Sardinian people inferred from whole-genome sequencing. BioRXiv 2016. Open access pre-pubLINK [doi:10.1101/092148]


The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

The authors call to some question the extreme simplicity of the three populations model of Lazaridis and subsequent studies. They do not flatly reject it but it seems that the lack of nuance bothers them a lot, as it does to me. This is quite clear when they find once and again Sardinian-Basque lines of relationship without going through Italian, Spaniard or French intermediaries, also when they face the issue of the largest Y-DNA haplogroups in the island, I2a1a (M26, almost exclusively a Sardinian and Pyrenean haplogroup) and R1b1a2 (M269), which are not typically associated with Neolithic farmers, suggesting that there is more to Neolithic settlement than meets the eye in the too simplistic three populations' model. They even seem to consider if Paleolithic peoples from Sardinia itself or maybe some other locations contributed heavily to what they feel is a sex-biased genetic pool.

They do confirm that Sardinians have both strong "Neolithic" (Stuttgart) and "Paleolithic" (Lochsbour) ancestry and no (negative even) "Steppe" (Yamnaya) one, although this last is truer for the most isolated sub-populations than for the more cosmopolitan ones. 

They also estimate that Sardinians have been generally isolated from the rest of Europeans for some 330 generations, what reads as approx. 9900 years, i.e. since the very early Neolithic settlement of the island. We would actually have to reduce that time span a bit but within reason, else it becomes Epipaleolithic in fact, what is most unlikely. Alternatively, as the main comparison is Northern Europe, this date could refer to the branching out of Painted-Linear (continental) and Impressed-Cardium (maritime) Neolithic cultures in the Aegean or the Balcans.

Oldest evidence for cooking in pots comes from Libya


Kambiz Karami at Anthropology.net (a most interesting blog to follow) mentioned this week that Libyan pottery remains, maybe as old as 10,000 years ago, have provided the oldest evidence of vegetable cooking of we know of, at least in pots (see below for the disclaimer). The remains indicate cooking of vegetables and meat and are associated to pictures of people gathering plants, as well as grinding stones (hand mills) with remains of such provisions.

Ref. Nature Plants.

Oddly enough, just two days later, he contradicted himself, mentioning that the charred remains of nuts and seeds from Palestine, dated from 780,000 years ago, actually provide the oldest evidence of vegetable cooking, even if it's clearly a more primitive way of cuisine and not yet at all the "refined" stew of ancient Libyans, which won them three stars in the Paleo-Michelin Guide for Nomads and five pitchforks in Popular Mesolithic Cuisine

Ref. PNAS.

Update (Jan 4): origin of Libyan and West Asian pottery could be Sudan

Jm8 mentions it in the comments, referencing to Anthromadness. I would need more data to judge (the ref. paper is behind paywall) but  it does sounds as probably correct to me, being Sudan/Nubia one of the earliest Mesolithic areas in the Western half of the Old World, one that is way too often and unfairly neglected but that definitely influenced the Levant prior to the development of Neolithic proper (what should explain a lot of things both linguistic and genetic).

Ancient aboriginal DNA from El Hierro (Canary Islands)

The island of El Hierro (lit. The Iron) is one of the westernmost of the Canary Islands. I have never visited but it seems to be very beautiful, far enough from the Sahara to enjoy a warm yet humid climate. It wasn't far enough to remain uninhabited however and now we get to know something more about its original dwellers, generally known as Guanches (although technically this name only applied to the inhabitants of La Palma originally).

Alejandra C. Ordóñez et al., Genetic studies on the prehispanic population buried in Punta Azul cave (El Hierro, Canary Islands). Journal of Archaeological Science 2016. Pay per viewLINK [doi:10.1016/j.jas.2016.11.004]


The aim of this study was to establish the genetic studies of the population from one of the most important known aboriginal funerary spaces of the island of El Hierro (Canary Islands), the Punta Azul cave, which harbors remains of 127 individuals. Sixty-one adult tibiae were examined, 32 left and 29 right. Radiocarbon dating yields an antiquity of 1015–1210 AD. We have obtained an overall success rate of 88.5% for the molecular sexing, and of 90.16% for the uniparental markers. Short tandem repeats (STR) profiles were also possible for 45.9% of the samples. This performance is a consequence of the good conservation of the bones in their archaeological context. The mtDNA composition of the sample is characterized by the complete fixation of the H1-16260 lineage. These results can be explained by a mixture of consecutive founding events, a bottleneck episode at the beginning of the colonization and/or as a consequence of genetic drift. Paternal lineages were also affected by these processes but in a less acute way. These differences lead us to propose social behaviors as an explanation for this difference. The maternal transmission of the lineages, mentioned in ethnohistorical sources of the Archipelago, could be an explanation. These results could be in agreement with endogamous practices, but the autosomal STR results indicate a relative high diversity. These results have allowed us to characterize the Punta Azul cave population and see the way in which geographical isolation, the process of adaptation and specific social behaviors affected the aboriginal population of the Island.

And now the interesting stuff, the findings:

As should be expected, the remote and rather small western island, which is the most direct threat to the security of the USA and the Western World in general because of the danger its volcano may slide into the Ocean and cause a huge tsunami of devastating consequences, something that no nuclear arsenal can do anything against, shows clear indication of very strong genetic drift relative to its relatives of the larger islands, caused either by founder effects and/or endogamous drift. Otherwise it is within the general patterns for the pre-colonial islanders. 

We see a lot of likely mtDNA H and certain Y-DNA R1b1a2. The Canary Islands were settled c. 1000 BCE (11,000 HE) by people arrived from what is now Morocco and the Western Sahara. They seem to retain a somewhat archaic genetic pool, relatively rich in Europe-related genetic elements, not so abundant at all today in Northwest Africa anymore, and by this I mean of course very especially Y-DNA haplogroups I and R1b. While we can still find some R1b in NW Africa, haplogroup I is almost impossible to find nowadays, yet it was present in the Canary Islands prior to European conquest and nearly disappeared afterwards (so it's definitely not a colonial input, accidentally misidentified, not at all). 

See also: Leherensuge: Ancient Guanche Y-DNA.

Iberomaurusian ancient mtDNA

This is an issue that has lingered for a long time in the online anthropology circles. Once upon a time (2005) there was online a presentation in which a good deal of mitochondrial DNA (HVS-I) sequences from the key Iberomaurusian (or Oranian) culture site of Taforalt (North Morocco) were (not too formally) published. Eventually this presentation became almost impossible to find... however now Rym Kefi (the original author if I remember correctly) and colleagues have got back to resurrect that important data set from oblivion, plus sequences from Afalou cave as well.

Rym Kefi et al., On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations. Forsenic Sciences Research 2016. Freely available at the time & space of writing thisLINK [doi:10.1080/24701394.2016.1258406]


The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000–11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000–10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations.

The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.

The bulk of the data is this (tables 1 and 2):

Notice that all sequences are "old style", i.e. HVS-I only, and that's why haplogroup assessment is not always 100% certain, with particular emphasis on the "CRS" sequences, which have been proven in some ancient cases to belong not to the modern normal (H1, rarely H2 o other H) but to a very rare modern haplotype within U*, AFAIK only preserved in Asturias but somewhat common in the Magdalenian of South Germany. 

In any case, that they produce 100% safe H1, H6, H14, etc. and, even more surprisingly, J and T2 variants, should make people think about the hidden Paleolithic mtDNA diversity in the wider Mediterranean area. And by this I do not just mean North Africa but also all Southern Europe, including many areas that can't be considered part of the Mediterranean basin, such as most of the crucial Franco-Cantabrian Region, the most densely populated province, by far, of post-LGM Upper Paleolithic Europe, source of several cultural waves (including the Solutrean one, almost certainly at the origin of Iberomaurusian), yet outrageously neglected by research.

Table 5 and other materials in the paper also deal with which modern populations appear closest to the Iberomaurusian ancient mtDNA pool and these are:
  1. Tuscans (0.00090)
  2. Catalans (0.00134)
  3. Galicians (0.00223)
  4. Sicilians (0.00377)
  5. El Alia (0.00699)
  6. Valencian (0.00787)
  7. Matmata (0.00788)
  8. Slougia (0.00831)
  9. Jerba Berbers (0.00934)
Figures in brackets are FST distances, the smaller the closer the match, statistically speaking. Populations in cursive are from Northwest Africa.

That is I'd say quite surprising because we tend to think of those near matches as quite impacted by Neolithic and post-Neolithic inflows, at least judging on other recent research. It seems that the debate on the origin of modern Europeans and North Africans refuses to come to a close, as different aspects of the evidence available may be somewhat contradictory. What do you make up of all this?

See also:

UPDATE: single marker inferred lineages (not always the haplogroup is reported correctly):

Down in the comments' section, Capra questions with good sense the certainty of inferred haplogroups. The most clear one is TafV27, claimed to be H6a1a8, which cannot actually be that (would need another HVS-I marker defining H6, which is missing), however this means that it must be HV0 and possibly V, a lineage that appears (per the aDNA literature) in the European Neolithic, already quite towards the West, out of nowhere, and that "nowhere" should not be West Asia, where it has never been sequenced, unlike K. 

I'm therefore reviewing here all the single-marker inferred haplogroups as carefully as possible, please double-check them and report if I seem to be committing any error:
  • AF22B - 16126C (reported as JT or H14b1) - JT(xJ,xT) or H14b1 indeed, notice that JT* was probably also one of the lineages described (also by the HVS-I method) for Nerja cave (Solutrean, same time frame), just across Alboran Sea (cf. Fernández-Domínguez 2005). Whether is one or the other or even something else, it's almost certain that the lineage was shared across the sea between Europe and Africa, what just makes total sense for this culture.
  • Taf55-IB - 16239T (reported as H1) - I actually get specific H1 variants (H1bf'bg'bh'ch specifically) or H17c. H sublineages in any case, unless it is an extinct or unreported R* lineage, most unlikely.
  • TafV27 - 16298C (reported as H6a1a8) - must be HV0, possibly even V, a distributed Euro-African lineage with three hotspots: Kabylia, Catalonia and Lappland. Per Caramelli 2003 and successor studies, this lineage was already present in Italy (Pagilicci cave) in the Gravettian era.
  • TafVIII - 16223T (reported as U4a2b) - It cannot be U4 at all because it lacks the HVS-I mutation 16356C. In fact the reverse 16223C mutation defines macro-haplogroup R, and I can't find any other matches within R, so it must be L3(xR), maybe N(xR) but maybe M or other L3. The possibilities are many, for example: N1, N2, N9, N11, etc. within N, a lot of possibilities within M, and also several within L3e'i'k'x(xL3x). The only thing we should be certain here is that it is not R and also not upstream of L3 (that's how good as it gets with HVS-I methodology, really). 
  • TafXXV3 - 16126C (reported as H14b1) - as with AF22B, it can be JT(xJ,xT) or H14b1 and again I must emphasize that there is an extremely good chance that this matrilineage had relatives in Iberia (Nerja) within the Solutrean culture.

In case you want to re-check, the best resource is of course PhyloTree.

IMPORTANT CAVEAT: the above update was done assuming they had fully sequenced the HVS-I, which is not that long, but it seems that in many cases (second column of the tables above) they have only sequenced up to the 16317 locus, what makes prediction of haplogroup even harder. That would explain their H6a1a8 prediction, although there's no way they can exclude the much more common HV0 (H6 is unheard of in North Africa). Thanks again to Capra for pointing that out.

Happy 12,017

Yeah, 12,017. Why not? And I do mean the year that begins today per the Gregorian Calendar.

This is a surprisingly well thought idea that some prehistorianists (i.e. those who like Prehistory, regardless of wage-earning profession) have proposed: to get rid of the clearly uncomfortable Christian Era, alias Roman Era, alias Common or Conventional Era (CE) by adding 10,000 years to it and roughly starting counting at Göbekli Tepe (approx. date, because it's impossible to pinpoint an exact date, but the same happens with the alleged birth of baby Jesus anyhow), without doubt the first "civilizational" type of monument ever built, incidentally getting rid of negative counting for at least the whole Holocene (a most convenient feature indeed). 

They propose to call it the "Human Era" (HE), although I'd rather think that the Human Era begins with humans and that would be c. 200,000 years ago for Homo sapiens and two million years ago for the overall Homo genus, Humankind generally speaking. So maybe it's better to call it the Monumental Era, the Megalithic (big stone) Era or just the Mega-Era, for short. It'd be ME in any case.

The proposal, as far as I can tell, was made by Kurzgesagt, one of the YouTube channels that provide a good mix of entertainment and information for people interested in history and prehistory, young and elderly alike:

And I like it quite a bit, of course. So maybe worth spreading around, don't you think? 

In any case, I wish you all a happy and productive new year, one in which things may hopefully change for the better and not for the worse, for a change. 

And, like in every New Year Day, the holiday where most work is made, because of that floating notion that you are supposed to made up for all the laziness and procrastination of the past year, I will now proceed to assault my quite fatty "to do" list, and tell you about things that you may or not know already but that I think are worth taking note of.

November 2, 2016

Main Neanderthal admixture episode was c. 100,000 years ago.

This is really nice to read, considering that the archaeological data strongly favors a single out-of-Africa migration around that date (c. 125 Ka to Arabia and Palestine, see this, this and this among others, c. 100 Ka to South and East Asia) and that my own genetic modeling on mitochondrial DNA also fits that chronology (unlike most "molecular clock" scholastic rantings that are sold as "scientific truth" with no substantive backing whatsoever).

Admittedly the paper is not new (was published in February) but you know I have been missing important stuff with my information-overload stress crisis, so I'm making up now. Thanks to Ryan for bringing this up.

Martin Kuhlwilm et al., Ancient gene flow from early modern humans into Eastern Neanderthals. Nature 2016. Pay per viewLINK [doi:10.1038/nature16544]


It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

As the title and the abstract say, Homo sapiens migrants out of Africa (i.e. into Asia and only later into its periphery) genetically influenced the branch of Neanderthals represented by the Altai specimen, what we can consider "Asian Neanderthals" but not the branch represented by El Sidrón and Vindija ("European Neanderthals"). This happened some 100 Ka ago, coincident with the archaeologically demonstrated dates for the out-of-Africa migration for our species and also likely Neanderthal-Sapiens hybrid fossils like Skhul-5 (right -- notice its lack of chin, a key and universal trait of H. sapiens, which allows us to give up with heavy browridges and other facial armature and still retain a strong bite, among other Neanderthaloid features, however it has a rounded and elevated skullcap with a high, almost vertical, forehead, a clear Sapiens trait). 

The flow was in both directions. I do not have access to the paper itself but it is clear in the supplemental material (EDF-1). This hybridization event was distributed quite evenly among all "Greater Asians" or "non-Africans" in our species. The slightly lower score in French is surely caused by Neolithic admixture later on, bringing African-like genetics to Europe, which are absent in most of Asia, as well as in aboriginal Australasia and America. 

Another apparent highlight in this paper (EDF-7) is that a second Neanderthal population, belonging to what I called above "European Neanderthals" (but related only to El Sidrón and not to Vindija) seems to have starred a second hybridization event affecting mostly Eastern populations (Han Chinese and Papuans in this paper's dataset). This, if confirmed, is quite unexpected and would require some explanation of the kind: there was a "European Neanderthal" population somewhere in Asia in the early times of Homo sapiens colonization and they got again admixed but this time affecting the derived populations in an irregular way. These irregularities would eventually be "flattened", I guess, at regional levels but for then the West Eurasian founders were out of the way. 

A somewhat related recent paper, also mentioned by Ryan, is S. Sankararaman et al., The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans (Current Biology 2016), also pay-per-view, so judging on supplemental materials only. I must say I don't like this one that much but at least table S2 offers a summary of the state of the art of estimates of Neanderthal and "Denisovan" (H. heidelbergensis) admixture in a lot of populations (and not just three). It is apparent there that there is more Neanderthal admixture towards the East of Asia or "Greater Asia", what is very much counterintuitive and demands that a Neanderthal population (a "European Neanderthal" one per Kuhlwilm's data) existed somewhere towards the East of Asia, enabling for this secondary Neanderthal admixture event. 

Perplexing maybe but that's what the data says. I wish we could find and sequence some of those Eastern Neanderthals which are so far just a genetic ghost, with the only possible known paleontological evidence being the Narmada skullcap, which is admittedly very much Neanderthal-like but is not associated in any way to Neanderthals' typical industry: the Mousterian, which has never been found east of Iran nor south of Mongolia. 

Some have argued that the Zhirendong jaw, one of the key evidences for c. 100 Ka H. sapiens settlement of much of Asia, is a hybrid one, with clear H. sapiens traits (among others it has a chin) but also maybe "archaic" traits (among others its chin is rather small). If so, then we may be at the same time in this case before evidence of both the early migration of our species, Homo sapiens, to East Asia (or SE Asia, as it's quite to the south of China) and the second admixture event with Neanderthals, with those ghostly Oriental Neanderthals, related to El Sidrón ones in the Far West, quite paradoxically, that we have yet to properly identify.