October 22, 2016

The 300 (improved) genomes project

I must make mention here of this study, which seems an attempt to improve the available datasets of global human genetics, particularly the widely used 1000 Genomes Project. It has some less striking but still interesting highlights.

Swapan Mallick et al., The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature, 2016. Pay per viewLINK [doi:10.1038/nature18964]


Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

The genomes and some other information seem to be available in their dedicated webpage.

One of the highlights is explicit in the abstract: the single African origin of Homo sapiens and the single out-of-Africa migration episode are confirmed. I didn't have any doubt but there have been occasional speculations, based on nothing worth considering, on the conjecture of more than one migration out of Africa before the Holocene, maybe affecting Australasian peoples. Not at all: it's all based on mere misunderstanding on how "racial" traits evolved, those remote isolated peoples basically allow us for a glimpse on the plausible phenotypes of the early Eurasian migrants, which were probably quite dark in skin pigmentation and most often had thinly curled hair like that of most Africans. In fact, I have argued on occasion that it is very possible that straight hair and its less extreme variants, wavy and widely curly hair, are Neanderthal genetic and phenotype influences, positively selected for some unclear reason, and not part of our African Homo sapiens heritage. 

The other highlight that I appreciate is that they find some errors in the 1000 Genomes Project, particularly affecting Australasians, Andamanese and some Africans (quite extreme among the Khoisan particularly). This is very apparent in this map and might explain some misleading and often puzzling conclusions made by some researchers, academic or amateur alike:

Otherwise I do not find their reconstructions of the paleo-history of Humankind, based only on autosomal DNA (not the best tool for such deep incursions, really), too helpful. But the most important thing is the existence and availability of a new, allegedly improved, global dataset.

October 21, 2016

Wisent co-existed with true bison already in the Paleolithic

A fascinating story this one indeed: the European bison or wisent has some ancestry related to the cow, evident in its mitochondrial DNA. This was already known but what wasn't known is that this distinct "hybrid" species of bison dated to the Upper Paleolithic. Thanks to the excellent records of anonymous prehistorical biologists who recorded them in Southwestern European rock art with great detail and naturalism, modern researchers have realized that the wisent, with its bovid heritage, existed already in the Upper Paleolithic. Ancient DNA recovery has now confirmed the artist's impression.

Julien Soubrier et al. Early cave art and ancient DNA record the origin of European bison. Nature communications, 2016. Open access → LINK [doi:10.1038/ncomms13158]


The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (< 11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).

The depictions of both types of bison are rather distinct but it seems nobody had noticed the difference until now, as the researchers explain in this article.

Fig. 1 - (a) Reproduction from Lascaux cave (France), from the Solutrean or early Magdalenian period (20,000 kya—picture adapted from ref. 53). (b) Reproduction from the Pergouset cave (France), from the Magdalenian period (<17,000 kya—picture adapted from ref. 54).

The ancient wisents sequenced now carry a distinct mtDNA haplogroup, called "clade X", which is sister to that of modern wisents (all descending from just 12 survivors). This wisent macro-haplogroup forms a clade with that of bovine cattle (cows of all sorts, both taurine and indicine) but they are joined only at the root, suggesting that the hybridization event that created the wisents as distinct species is very old, just a bit more recent than the divergence of cow and bison.

Fig. 2 - (a) Phylogenetic tree inferred from bovine mitochondrial control region sequences, showing the new clade of bison individuals. The positions of the newly sequenced individuals are marked in red for CladeX. (b) Bovine phylogeny estimated from whole-mitochondrial genome sequences, showing strong support for the grouping of wisent and CladeX with cattle (cow) and zebu. For both trees (a,b) numbers above branches represent the posterior probabilities from Bayesian inference, numbers below branches represent approximate likelihood ratio test support values from maximum-likelihood analysis and scale bars represent nucleotide substitutions per site from the Bayesian analysis. (c) Maximum-clade-credibility tree of CladeX and wisent estimated using Bayesian analysis and calibrated with radiocarbon dates associated with the sequenced bones. Dates of samples older than 50 kyr were estimated in the phylogenetic reconstruction. (d) Map showing all sampling locations, using the same colour code (red for CladeX, orange for wisent and blue for steppe bison).

So it is not random auroch hybridization but a very specific and very ancient episode of admixture between the ancestors of bisons and cows.

The two species appear to have distinct ecological niches:

The detailed records of the southern Ural sites allow the timing of the population replacements between steppe bison and wisent to be correlated with major palaeoenvironmental shifts, revealing that the wisent was associated with colder, more tundra-like landscapes and absence of a warm summer.

This pattern seems to correspond with the periods in which the two species are portrayed in rock art, as two of the researchers explain in this video (third part):

Post-statement: I must say that, on second thought, I'm not really convinced by the claim of wisent corresponding to colder periods. In fig. 1 above it is apparent that it is the steppe bison which corresponds to the last glacial maximum (LGM) in Southwestern Europe and not the wisent, which only shows up after the end of this coldest period. 

I wonder if the researchers are explaining themselves well enough on this aspect or if it is a case of wishful thinking, maybe caused by different conditions in SW Europe (where the rock art is) and the Southern Urals (where most of the archaeogenetic and paleontological data comes from). 

At the very least, judging on fig. 1, it would be the steppe bison the one corresponding with the coldest spell and the wisent the one corresponding to more temperate conditions. Can someone explain me what is going on here?

Armintxe: new rock art site discovered in the Basque Country

A week ago a new rock art site was revealed to exist right in the town of Lekeitio (Biscay). The art, estimated to be from some 14,000 years ago (Magdalenian culture), is made up of several groups of engraved animals: bisons, horses, goats and deers. The cave is not far from other known sites like Lumentxa, Atxurra and Santa Catalina.

Video of the cave and art[es]:

More information:
Pileta de Prehistoria[es] (has several videos and news from several sources, quite extensive)

October 9, 2016

A 14.000 year old human settlement in Argentina


Although the paper claims this site as the signature of arrival of our species to the South Cone (southern region of South America), there is another site with quite apparently older dates: Monte Verde (Chile), that cannot be ignored. In any case, it is a quite interesting data point for the peopling of America and the oldest one known East of the Andes.

Gustavo G. Politis et al., The Arrival of Homo sapiens into the Southern Cone at 14,000 Years Ago. PLoS ONE, 2016. Open accessLINK [doi:10.1371/journal.pone.0162870]


The Arroyo Seco 2 site contains a rich archaeological record, exceptional for South America, to explain the expansion of Homo sapiens into the Americas and their interaction with extinct Pleistocene mammals. The following paper provides a detailed overview of material remains found in the earliest cultural episodes at this multi-component site, dated between ca. 12,170 14C yrs B.P. (ca. 14,064 cal yrs B.P.) and 11,180 14C yrs B.P. (ca. 13,068 cal yrs B.P.). Evidence of early occupations includes the presence of lithic tools, a concentration of Pleistocene species remains, human-induced fractured animal bones, and a selection of skeletal parts of extinct fauna. The occurrence of hunter-gatherers in the Southern Cone at ca. 14,000 cal yrs B.P. is added to the growing list of American sites that indicate a human occupation earlier than the Clovis dispersal episode, but posterior to the onset of the deglaciation of the Last Glacial Maximum (LGM) in the North America.

September 8, 2016

Genetic structure in South-Eastern Africa


Another quite interesting paper on Khoesan and Southern African genetics:

Caitlin Uren et al., Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries. Genetics 2016. Freely accessibleLINK [doi:10.1534/genetics.116.187369]


Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.
Figure 2
Five spatially distinct ancestries indicate deep population structure in southern Africa. Using global ancestry proportions inferred from ADMIXTURE k = 10, we plot the mean ancestry for each population in southern Africa. The five most common ancestries in southern Africa, from the Affymetrix HumanOrigins data set, are shown separately in A–E. The x- and y-axes for each map correspond to latitude and longitude, respectively. Black dots represent the sampling location of populations in southern Africa. The third dimension in each map (depth of color) represents the mean ancestry proportion for each group for a given k ancestry, calculated from ADMIXTURE using unrelated individuals, and indicated in the color keys as 0–100% for five specific k ancestries. Surface plots of the ancestry proportions were interpolated across the African continent.

See also:

August 29, 2016

Gobero (Green Sahara key site) documentary

This site of Gobero (Niger) was news in the archaeology and anthropology circles a few years ago and today I stumbled on this quite nice video documentary on it that I believe will be of interest for many readers:

August 21, 2016

Paleolithic European mtDNA lineage U5b2c1 in Carthaginian man


Elizabeth A. Matisoo-Smith et al. A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa. PLoS ONE 2016. Open accessLINK [doi:10.1371/journal.pone.0155046]


While Phoenician culture and trade networks had a significant impact on Western civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa.

The lineage is the same one as La Braña 1, an Epipaleolithic man buried in a cave at the mountains NE of León. Its presence on a Carthaginian from the 6th century BCE almost certainly indicates that he had native Iberian maternal ancestry, that his family had arrived to Carthage from Gadir (modern Cádiz) or some of the other Phoenician colonies of Andalusia. The location of his burial at the acropolis and the wealth of the burial goods indicate that he belonged to the highest social elite of the still incipient Carthaginian empire. He has been nicknamed "Ariche" (the loved one) and his face reconstructed as you can see in this blog.

Thanks to Jamel of Lapurdi for the reference an a nice related discussion.

All the Neolithic and Chalcolithic of Ireland in a single paper

This entry should be a "quickie" because I wouldn't even know where to begin in order to analyze this comprehensive synthesis and not at all because it is a lesser study, all the oposite. Just to say that the average reader of this blog will want to read it, much more if they are Irish.

However I think that the paper raises some interesting questions regarding the chronology of "modern genetic Irishness" and the arrival of the Y-DNA lineage R1b to the island, which I cast below for your insights.

T. Rowan McLaughling et al., The Changing Face of Neolithic and Bronze Age Ireland: A Big Data Approach to the Settlement and Burial Records. Journal of World Prehistory 2016. Open accessLINK [doi:10.1007/s10963-016-9093-0]


This paper synthesizes and discusses the spatial and temporal patterns of archaeological sites in Ireland, spanning the Neolithic period and the Bronze Age transition (4300–1900 cal BC), in order to explore the timing and implications of the main changes that occurred in the archaeological record of that period. Large amounts of new data are sourced from unpublished developer-led excavations and combined with national archives, published excavations and online databases. Bayesian radiocarbon models and context- and sample-sensitive summed radiocarbon probabilities are used to examine the dataset. The study captures the scale and timing of the initial expansion of Early Neolithic settlement and the ensuing attenuation of all such activity—an apparent boom-and-bust cycle. The Late Neolithic and Chalcolithic periods are characterised by a resurgence and diversification of activity. Contextualisation and spatial analysis of radiocarbon data reveals finer-scale patterning than is usually possible with summed-probability approaches: the boom-and-bust models of prehistoric populations may, in fact, be a misinterpretation of more subtle demographic changes occurring at the same time as cultural change and attendant differences in the archaeological record.

The study should be very useful to anyone trying to understand the prehistory of Ireland, not the least because of its many maps and this extremely cool sequential maps video from pre-Neolithic times (5th millennium BCE) to the gates of the Bronze Age (early 2nd millennium BCE). Notice that in the Isles they tend to call "Bronze Age" to the Chalcolithic (Copper and Stone Age) and hence the title, which is a bit misleading.

An example of the very cool and highly informative maps and data you'll find in this study:
Fig. 3 - Map of Ireland showing Early Neolithic sites


Depopulation and resettlement? When?

An intriguing issue is the boom and bust cycles, particularly the almost total absence of signs of human activity around the end of the 4th millennium (3300-3000), suggesting maybe a depopulation after the first farmer colonization (?). There are clear booms around 4000, 3700, 3500, 2900, 2500 and since 2200 (Bell Beaker era). All this is something to chew about.

Particularly I'd raise the following question here: we know that a woman from c. 3400-3100 BCE (just at the depopulation gap?) was a typical Neolithic European, most similar to SE Spaniards and Sardinians, and that a man from c. 2200-1500 (Bell Beaker boom) was virtually identical to modern Irish and "British Celts" like Scots, Welsh and Cornish, carrying the common and controversial R1b patrilineage. 

The initial reading many of us made was that these new genetics may have arrived with Bell Beaker and that maybe Bell Beaker was more influential in terms demographic than we used to think, at least in Ireland. However, with this archaeological sequence on hand it seems at least reasonable to think that the major resettlement of an almost deserted Ireland happened after 3000 BCE but significantly earlier than the Bell Beaker phenomenon, which only reaches Northern Europe (Ireland included) c. 1500 BCE. What's your opinion?

Genetic prehistory of European bovine cattle


Another study on European cattle, suggesting little to no admixture with aboriginal aurochs. However, as far as I can see, they did not directly compare with European aurochsen, so I'm rather skeptic, as their conclusions seem to derive only from modeling out of an incomplete dataset.

Amelie Scheu et al., The genetic prehistory of domesticated cattle from their origin to the spread across Europe. BMC Genetics 2016. Open accessLINK [doi:10.1186/s12863-015-0203-2]



Cattle domestication started in the 9th millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication.


Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE.


The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers.

Figure 1

MDS Plot of d-loop sequences from 13 spatiotemporal groups of ancient domesticated cattle. The MDS plot is based on Reynolds’ FST. Numbers represent the age of samples in BCE per group; brackets contain the number of sequences per group.

Mitochondrial DNA of ancient Tocharians


It seems there is still something to learn about the ancient Tocharian mummies of Uyghuristan:

Chunxiang Li et al., Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China. BMC Genetics 2016. Open accessLINK [doi:10.1186/s12863-015-0237-5]



The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers.


Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5.


Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

African admixture events


This paper is probably of interest to many but I don't have the insight to make a proper analysis. Just to mention that I feel deeply uncomfortable with the use of the "Sub-Saharan" term, which has so many wrong ideas attached to it, particularly the word "sub" (under, below) that it really irks me. Why not Trans-Saharan or Ultra-Saharan?, very Roman and not the least Eurocentric but definitely not just all kinds of wrong, as "Sub" is. Why not Tropical and Southern Africa?

Sub-Saharan is not just implicitly Eurocentric and almost certainly racist (sub-what?! subordinated?, sub-human maybe?) but, most importantly, it is geometrically and geographically very wrong. The South is not "under" the North: they are all on the same spheroid surface or equivalent cuasi-plane. Even a primary school student knows that!

Anyhow, this is what they have to say in minimalistic terms:

George BJ Busby et al., Admixture into and within sub-Saharan Africa. eLife 2016. Open access LINK [doi: eLife 2016;5:e15266]

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

Figure 4. Inference of admixture in sub-Saharan African using GLOBETROTTER. (A) For each group we show the ancestry region identity of the best matching source for the first and, if applicable, second events. Events involving sources that most closely match FULAI and SEMI-BANTU are highlighted by golden and red colours, respectively. Second events can be either multiway, in which case there is a single date estimate, or two-date in which case 2ND EVENT refers to the earlier event. The point estimate of the admixture date is shown as a black point, with 95% CI shown with lines. MIXTURE MODEL: We infer the ancestry composition of each African group by fitting its copying vector as a mixture of all other population copying vectors. The coefficients of this regression sum to 1 and are coloured by ancestry region. 1ST EVENT SOURCES and 2ND EVENT SOURCES show the ancestry breakdown of the admixture sources inferred by GLOBETROTTER, coloured by ancestry region as in the key top right. (B) and (C) Comparisons of dates inferred by MALDER and GLOBETROTTER. Because the two methods sometimes inferred different numbers of events, in (B) we show the comparison based on the inferred number of events in the MALDER analysis, and in (C) for the number of events inferred by GLOBETROTTER. Point symbols refer to populations and are as in Figure 1 and source data can be found in Figure 4—source data 1

Neolithic DNA from Southern Anatolia

I know, I know: I'm decaying into a total procrastinator. I don't have any excuse other than I don't feel like blogging as of late: neither on anthropology nor on politics. I rather feel like learning new stuff and playing, rather than writing and I lack of the structured environment to force myself to do otherwise than what I feel like most of the time. Being of compulsive temperament only worsens things.

I also know that this is not the proper way to start an article. Yes, I know. Do I even care?

So getting to mention now some of the stuff that I have not discussed in these last months and is definitely worth posting about. First of all this key study on more easterly Anatolian early farmers than those seen so far.

Intriguingly they are notoriously similar to those sequenced farther West (see here), what seems to support the model of Anatolian origin of European Neolithic peoples, largely ancestral to modern Europeans. However even Western Anatolian early farmers show already some extra admixture with the Paleoeuropean "WHG" component relative to their Southern Anatolian precursors. So, as the authors suggest, admixture between immigrant farmers and native foragers was a gradual and continuous process beginning in Asia Minor itself.

Gülşah Merve Kılınç, Ayça Omrak, Füsun Özer et al., The Demographic Development of the First Farmers in Anatolia. Current Biology 2016. Open accessLINK [doi:10.1016/j.cub.2016.07.057]


The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [ 1–3 ]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [ 4 ]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.

Autosomal DNA

Maybe the most informative graph is this one (fig. 2):

Genetic Structure and Diversity of Central Anatolian Neolithic Populations
(A) PCA on contemporary west Eurasian populations onto which a total of 85 ancient individuals are projected from this study and previous studies. See Table S1 for number of SNPs per individual. Neighboring modern populations and ancient Anatolian populations are shown encircled. Modern population names are in italics.
Etc. (not so interested here in B, C and D, legend too long, check in the original paper)
Click to expand

It is interesting that, in spite of the Anatolian origin of this ancient ancestral population, they do not tend so much to modern Anatolian Turks but rather to Levant populations like Cypriots (closest ones), Lebanese, Palestinians, etc.

This is probably because, even if early Neolithic peoples of the Levant were not quite like them (see here again) they had become almost like them before the Bronze Age because of regional admixture, which I understand was mostly (but not only) north-to-south flow.

Notice that the Boncuklu (Bon) people had very low genetic diversity and they seem to be a dead end rather than directly ancestral. Instead, the Tepecik-Çiftilik (Tep) population seems a good proxy for the ancestors of Neolithic peoples of Western Anatolia and Europe. 

When we think about South Anatolia Neolithic, we usually think first and foremost about the famous Çatalhöyük site. Well, this ancient settlement is in the area of Boncuklu (to the West, both are near Konya) rather than that of Tepecik-Çiftilik (to the East, near Niğde), so it is quite possible that it is another demographic dead end, related but not directly ancestral to mainline European Neolithic. 

Personally I still think they could well have migrated at least partly by boat, along the southern Turkish coast but, until new data comes, I may need to alter my hypothesis of the ultimate origin being in the Northern Levant (Syria, Lebanon, Cyprus even) rather than Anatolia. These people of Tepecik-Çiftilik were, if not direct ancestors at least very closely related to the actual source population, which may well have lived closer to the coast in any case.

Mitochondrial DNA

The newly sequenced South Anatolian farmers had some of the lineages that were later present in Hungary's and Germany's "Danubian Neolithic", notably the now rare N1a1a1, found in 4/9 samples in this study. Also present were K1a (3/9, incl. one K1a12a), U3 (1/9) and N1a1b (1/9).

So it is time to dismiss the hypothesis that claimed N1a1a1 as a European aboriginal lineage: it came with the immigrant farmers and now there can be no doubt about it.

June 26, 2016

Ancient genomes from Neolithic West Asia

This week we got to know a lot more about the genetics of ancient West Asians, from the Mesolithic, Neolithic and later times. All in a single major study:

Iosif Lazaridis et al., The genetic structure of the world's first farmers. BioRxiv 2016. Freely accessible (pre-pub)LINK [doi: http://dx.doi.org/10.1101/059311]


We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.


  • There were (at least) two clearly distinct populations in West Asia in the Mesolithic and Early Neolithic times.
  • Both populations contributed to the West Anatolian farmers that are precursors of the settlers of Neolithic Europe.
  • The so-called "Basal Eurasian" component is not yet clarified if it is something local or admixture with Africans or both. However it is clear that it is associated with reduced Neanderthal admixture.
  • West Eurasian genetic composition can be now understood quite well as the mixture from four sources: two West Asian ones, favored by the Neolithic revolution, and two Paleo-European ones.

This graphic shows pretty well how the ancient populations of West Eurasia are expressed as a mixture of those four founder populations:

That is if you can get through the nomenclature, which is inherited in many cases from a long array of recent studies. I'm not even sure myself in many cases what samples exactly and where from are thrown in each category. But the most important part is that Iran_N and Levant_N are the two Neolithic-specific founder populations of the Fertile Crescent (yeah, N stands for "Neolithic", not "North") and that the other two founder populations from pre-Neolithic Europe are WHG (Epi-Magdalenian peoples from Western and Central Europe) and EHG (Eastern European hunter-gatherers, of Epigravettian culture and maybe even proto-Uralic in one case).

Then we see in the case of Europe how:

1. Anatolia_N (precursors of mainline European Neolithic) are a mix of both West Asian farmer groups, plus a sizable fraction of Western Paleo-european ancestry already.

2. This fraction of Western Paleoeuropeanness increases as the farmers expanded into Europe (EN) and then as there was probably some backflow of Western origins in relation to Megalithism and Bell Beaker (MNChL). But in general remains the same basic genetic composition and in no known case incorporates any Eastern Paleoeuropean component at all, not yet.

3. It is only with the Indoeuropean ("Kurgan") invasions reflected in the category LNBA, when the EHG component begins feeling very important in Europe. If I'm correct, all those samples are from Germany other areas of Central and North Europe, with the Iberian and Italian ones of similar chronology placed in the MNChL tag instead. The LNBA/MNChL contrast is not a strictly chronological analysis but an analysis by categories of ancestry that do overlap in time.

4. In Armenia instead, we see a decrease of the minor EHG component but then an increase in the MLBA ("middle and late Bronze Age") when Armenians arrive from the Balcans and Phrygia, conquering the pre-existing Hurro-Urartean peoples (whose language was probably related to Chechen and other NE Caucasian languages), which should correspond to the formation of Urartu and more specifically to the Hayasa-Azzi and Shupria stages, both considered Urartean (Hurrian). The WHG and Levant-N components we see since the Chalcolithic is similar to what we see in West Anatolia and probably reflect interactions corresponding to Central-Eastern Anatolia, Kurdistan and Syria, for which we have no direct ancient data yet.

Ancient samples (colored and labeled) projected on a PCA of modern West Eurasian populations (in gray):

For a reference on which are the modern populations in gray, a good reference is this older but fully labeled PCA by Olalde.

Briefly: Natufians fall on top of modern Palestinians, their slightly admixed Neolithic descendants fall between Palestinians and Jews, Middle Neolithic European Farmers fall on top of Sardinians, the so-called Europe-Steppe continuum (early Western Indoeuropeans) fall between Central Europe, France and the Balcans, most Western Europeans do not overlap with ancient samples but appear to have even greater Paleoeuropean admixture instead, etc.

Y-DNA Haplogroups

Iranian Mesolithic and Neolithic samples carried the following patrilineages:
  • Mesolithic: J(xJ2a1b3,J2b2a1a1)
  • Ganj Dareh Neolithic: P1(xQ,R1b1a2,R1a1a1b1a1b,R1a1a1b1a3a,R1a1a1b2a2a) and an undefined CT
  • Late Neolithic: G2a1(xG2a1a)

Meanwhile Palestinian Mesolithic and Neolithic samples carried: 

  • Natufian (Mesolithic): E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), E1b1(xE1b1a1,E1b1b1b1), E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), plus two undefined CT.
  • Pre-Pottery Neolithic B/C: H2, E(xE2,E1a,E1b1a1a1c2c3b1,E1b1b1b1a1,E1b1b1b2b), E1b1b1, T(xT1a1,T1a2a), E1b1b1(xE1b1b1b1a1,E1b1b1a1b1,E1b1b1a1b2,E1b1b1b2a1c), plus three ill-defined CT.

CT is the main pan-Eurasian macro-haplogroup and is not informative, except in Palestine because it implies exclusion of E.

Otherwise we see an important presence of E (mostly E1b1b) a lineage we know was carried by early farmers into Europe and that has ultimately African origins. It probably indicates migration of NE Africans into Palestine in the Mesolithic, something also supported by Archaeology. However these NE Africans were surely already mixed with Eurasian ancestry, which probably arrived to the Nile Basin in the early LSA, some 50-40 Ka ago. So it's a complex story of multiple admixture events in the continental crossroads that is Egypt and also Palestine and other nearby areas.

We also see G2a1 in Late Neolithic Iran, and this one is the main lineage brought to Europe by the early farmers if we are to judge on known ancient sequences (today it is not more important that E1b but it is maybe more evenly distributed). However we only see it in the Late Neolithic, so it may have originated further west.

We see too little J, only J(xJ1a,J2a1,J2b) in Chalcolithic Iran and in Bronze Age Jordan: J(xJ1,J2a,J2b2a) again and J1(xJ1a). I guess that a lot remains to be researched on this issue because J is by far nowadays the most common haplogroup of West Asia, and also impacted Europe and South Asia (J2) and North and NE Africa (J1).

On the issue of "Basal Eurasian": African or West Asian?

The question remains unanswered, as I said before but there are two clues: on one side the presence of E1b in Mesolithic and Neolithic Palestine clearly supports a direct NE African influence, also backed by archaeological evidence. But there is some nuance in the issue of FST distances that I want to highlight.

The distances are available in a very extensive supplementary table, so I took just a few to get a better understanding, not only of this issue but in general of the genetic distances of the four founder populations:

Quite ironically it is not the Natufians who are the closest to the African reference population (Yoruba) but the CHG, Iran-N and Levant-N groups. In fact the Natufians are the most distant ones after the WHG population. However this is tricky because the affinity to Yoruba may also be caused by the "ghost" Basal Eurasian population, claimed first of all by Lazaridis 2014, which would be a remnant of the Out of Africa Migration (not strictly African but close enough and impossible to discern from true African admixture in most analyses).

So we may imagine that the "Highlander" (CHG and Iran-N) populations were somehow influenced by that Basal Eurasian ghostly population, which might have survived in the Persian Gulf oasis, for example. Or whatever else.

The presence of the same or similar element in Levant-N reflects possibly admixture with Iran-N or a similar population, something that is implicit in the table above but I'll address below more explicitly.

If there is (and there must be, because of Y-DNA E1b) some African admixture in the Natufian population, it was very diluted already in the autosomal (general DNA) aspect before farming began.

Update (Jul 2): all the four paragraphs above are possibly misleading to some extent because, as several commenters have rightfully pointed out, generic drift alone just causes the effect of increased distance to general reference populations like Yoruba and Han, this genetic drift is caused by relative isolation, so it seems that Magdalenian Europeans (WHG) and Natufian Palestinians (Natufian) were both more isolated populations in general terms than the Iran-Caucasus-Eastern Europe ones, whose sheer numbers apparently kept them more similar to the generic root of Humankind, less endogamous. 

However, per archaeology, such "sheer numbers" are not to be expected in that area, rather the opposite (Western Europe and Palestine are much more richer areas in terms archaeological, suggesting denser populations). So the question remains open as far as I can tell but it should be discerner with more precise tools than mere FST.

A visual of smallest genetic distances between (each "-" represents 0.01 in the table above):

a) Ancient West Asians:

Neolithic peoples of West Asia, even if different, are closer among them than their pre-Neolithic precursors.

b) Pre-Neolithic West Eurasians:

The distances between Natufians and everyone else are comparable to those with Han Chinese, however only in the case of the populations that appear to have extra affinity to East Asia (Iran, Caucasus and Eastern Europe), otherwise it is smaller.
All four populations were distant enough from each other to be considered clearly distinctive. Even EHG and WHG were quite dissimilar.

c) The four West Eurasian founders considered above:

There is much greater similitude between Iran and Levant Neolithic peoples than between their Mesolithic precursors. This implies some sort of intense admixture as agriculture and herding developed. Not enough to erase the differences but enough to blur them significantly.

Genetic influence from East Asia or a related population is also apparent in all Northeastern populations but even more so in Iran Neolithic. Why?

There is much more in the study and supp. materials but I can only review so much.