Sea Peoples behind Philistines were Aegeans, including R1b-M269 lineages

New open access paper Ancient DNA sheds light on the genetic origins of early Iron Age Philistines, by Feldman et al. Science Advances (2019) 5(7):eaax0061.

Interesting excerpts (modified for clarity, emphasis mine):

Here, we report genome-wide data from human remains excavated at the ancient seaport of Ashkelon, forming a genetic time series encompassing the Bronze to Iron Age transition. We find that all three Ashkelon populations derive most of their ancestry from the local Levantine gene pool. The early Iron Age population was distinct in its high genetic affinity to European-derived populations and in the high variation of that affinity, suggesting that a gene flow from a European-related gene pool entered Ashkelon either at the end of the Bronze Age or at the beginning of the Iron Age. Of the available contemporaneous populations, we model the southern European gene pool as the best proxy for this incoming gene flow. Last, we observe that the excess European affinity of the early Iron Age individuals does not persist in the later Iron Age population, suggesting that it had a limited genetic impact on the long-term population structure of the people in Ashkelon.

Ancient genomes (marked with color-filled symbols) projected onto the principal components inferred from present-day west Eurasians (gray circles). The newly reported Ashkelon populations are annotated in the upper corner.

Genetic discontinuity between the Bronze Age and the early Iron Age people of Ashkelon

In comparison to ASH_LBA, the four ASH_IA1 individuals from the following Iron Age I period are, on average, shifted along PC1 toward the European cline and are more spread out along PC1, overlapping with ASH_LBA on one extreme and with the Greek Late Bronze Age “S_Greece_LBA” on the other. Similarly, genetic clustering assigns ASH_IA1 with an average of 14% contribution from a cluster maximized in the Mesolithic European hunter-gatherers labeled “WHG” (shown in blue in Fig. 2B) (15, 22, 26). This component is inferred only in small proportions in earlier Bronze Age Levantine populations (2 to 9%).

In agreement with the PCA and ADMIXTURE results, only European hunter-gatherers (including WHG) and populations sharing a history of genetic admixture with European hunter-gatherers (e.g., as European Neolithic and post-Neolithic populations) produced significantly positive f4-statistics (Z ≥ 3), suggesting that, compared to ASH_LBA, ASH_IA1 has additional European-related ancestry.

We find that the PC1 coordinates positively correlate with the proportion of WHG ancestry modeled in the Ashkelon individuals, suggesting that WHG reasonably tag a European-related ancestral component within the ASH_IA1 individuals.

We plot the ancestral proportions of the Ashkelon individuals inferred by qpAdm using Iran_ChL, Levant_ChL, and WHG as sources ±1 SEs. P values are annotated under each model. In cases when the three-way model failed (χ2P < 0.05), we plot the fitting two-way model. The WHG ancestry is necessary only in ASH_IA1.

The best supported one (χ2P = 0.675) infers that ASH_IA1 derives around 43% of ancestry from the Greek Bronze Age “Crete_Odigitria_BA” (43.1 ± 19.2%) and the rest from the ASH_LBA population.

(…) only the models including “Sardinian,” “Crete_Odigitria_BA,” or “Iberia_BA” as the candidate population provided a good fit (χ2P = 0.715, 49.3 ± 8.5%; χ2P = 0.972, 38.0 ± 22.0%; and χ2P = 0.964, 25.8 ± 9.3%, respectively). We note that, because of geographical and temporal sampling gaps, populations that potentially contributed the “European-related” admixture in ASH_IA1 could be missing from the dataset.

The transient impact of the “European-related” gene flow on the Ashkelon gene pool

The ASH_IA2 individuals are intermediate along PC1 between the ASH_LBA ones and the earlier Bronze Age Levantines (Jordan_EBA/Lebanon_MBA) in the west Eurasian PCA (Fig. 2A). Notably, despite being chronologically closer to ASH_IA1, the ASH_IA2 individuals position closer, on average, to the earlier Bronze Age individuals.

See more information on Y-DNA SNP calls, including ASH067 as R1b-M269 (xL151).

The transient excess of European-related genetic affinity in ASH_IA1 can be explained by two scenarios. The early Iron Age European-related genetic component could have been diluted by either the local Ashkelon population to the undetectable level at the time of the later Iron Age individuals or by a gene flow from a population outside of Ashkelon introduced during the final stages of the early Iron Age or the beginning of the later Iron Age.

By modeling ASH_IA2 as a mixture of ASH_IA1 and earlier Bronze Age Levantines/Late Period Egyptian, we infer a range of 7 to 38% of contribution from ASH_IA1, although no contribution cannot be rejected because of the limited resolution to differentiate between Bronze Age and early Iron Age ancestries in this model.

Hg. R1b-M269 and the Aegean

I already predicted this relationship of Philistines and Aegeans (Greeks in particular) months ago, based on linguistics, archaeology, and phylogeography, although it was (and still is) yet unclear if these paternal lineages might have come from other nearby populations which might be descended from Common Anatolians instead, given the known intense contacts between Helladic and West Anatolian groups.

The alternative view: The Sea Peoples can be traced back to the Aegean, so they could also have consisted of Luwian petty kingdoms, who had formed an alliance and attacked Hatti from the south.

The deduction process for the Greek connection was quite simple:

Palaeo-Balkan populations

We know that R1b-Z2103 expanded with Yamna, including West Yamna settlers: they appear in Vučedol, which means they formed part of the earliest expansion waves of Yamna settlers into the Carpathian Basin, and they also appear scattered among Bell Beakers (apart from dominating East Yamna and Afanasevo), which suggests that they were possibly one of the most successful lineages during the late Repin/early Yamna expansion.

The “Steppe ancestry” associated with I2a-L699 samples among Balkan BA peoples may have also been associated with recent Bronze Age expansions, and this haplogroup’s presence among modern Balkan peoples may also suggest that it expanded with Palaeo-Balkan languages. Nevertheless, we don’t know which specific lineages and “Steppe ancestry” they represent, sadly.

These samples may well be related to remnants of previous Balkan populations like Cernavodă or Ezero, because there has been no peer-reviewed attempt at distinguishing Khvalynsk-/Novodanilovka- from Sredni Stog- from Yamnaya-related populations (see here), and some groups that are associated with this ancestry, like Corded Ware, are known to be culturally distinct from Yamna.

In any case, Proto-Greeks from the southern Balkans (say, Sitagroi IV and related groups) are probably going to show, based on Palaeo-Balkan substrate and Pre-Greek substrate and on the available Mycenaean samples, a process of decreasing proportion of R1b-Z2103 lineages relative to local ones, and a relatively similar cline of Yamna:EEF ancestry from northern to southern areas, at least in the periods closest to the Yamna expansion.

NOTE. The finding of “archaic” R1b-L389 (R1b-V1636) and R1a-M198 subclades among modern Greeks and the likely Neolithic origin of these paternal lineages around the Caucasus suggest that their presence in Greece may be from any of the more recent migrations that have happened between Anatolia and the Balkans, especially during the Common Era, rather than Indo-Anatolian migrations; probably very very recently.

Bronze Age cultures in the Balkans and the Aegean. See full map including ancient samples with Y-DNA, mtDNA, and ADMIXTURE.

Minoans and haplogroup J

In the Aegean, it is already evident that the population changed language partly through cultural diffusion, probably through elite domination of Proto-Greek speakers. Whether that happened before the invasion into the Greek Peninsula or after it is unclear, as we discussed recently, because we only have one reported Y-chromosome haplogroup among Mycenaeans, and it is J (probably continuing earlier lineages).

Now we have more samples from the so-called Emporion 2 cluster in Olalde et al. (2019), which shows Mycenaean-like eastern Mediterranean ancestry and 3 (out of 3) samples of haplogroup J, which – given the origin of the colony in Phocea – may be interpreted as the prevalence of West Anatolian-like ancestry and lineages in the eastern part of the Aegean (and possibly thus south Peloponnese), in line with the modern situation.

NOTE. It does not seem likely that those R or R1b-L23 samples from the Emporion 1 cluster are R1b-Z2103, based on their West European-like ancestry, although they still may be, because – as we know – ancestry (unlike haplogroup) changes too easily to interpret it as an ancestral ethnolinguistic marker.

PCA of ancient samples related to the Aegean, with Minoans, Mycenaeans (including the Emporion 2 cluster in the background) Anatolia N-Ch.-BA and Levantine BA-LBA populations, including Tel Shadud samples. See more PCAs of ancient Eurasian populations.

Greeks and haplogroup R1b-M269

Therefore, while the presence of R1b-Z2103 among ancient Balkan peoples connected to the Yamna expansion is clear, one might ask if R1b-Z2103 really spread up to the Peloponnese by the time of the Mycenaean Civilization. That has only one indirect answer, and it’s most likely yes.

We already had some R1b-Z2103 among Thracians and around the Armenoid homeland, which offers another clue at the migration of these lineages from the Balkans. The distribution of different “archaic” R1b-Z2103 subclades among modern Balkan populations and around the Aegean offered more support to this conclusion.

But now we have two interesting ancient populations that bear witness to the likely intrusion of R1b-M269 with Proto-Greeks:

An Ancient Greek of hg. R1b

A single ancient sample supports the increase in R1b-Z2103 among Greeks during the “Dorian” invasions that triggered the Dark Ages and the phenomenon of the Aegean Sea Peoples. It comes from a Greek lab study, showing R1b1b (i.e. R1b-P297 in the old nomenclature) as the only Y-chromosome haplogroup obtained from the sampling of the Gulf of Amurakia ca. 470-30 BC, i.e. before the Roman foundation of Nikopolis, hence from people likely from Anaktorion in Ancient Acarnania, of Corinthian origin.


Even with the few data available – and with the caution necessary for this kind of studies from non-established labs, which may be subject to many different kinds of errors – one could argue that the western Greek areas, which received different waves of migrants from the north and shows a higher distribution of R1b-Z2103 in modern times, was probably more heavily admixed with R1b-Z2103 than southern and eastern areas, which were always dominated by Greek-speaking populations more heavily admixed with locals.

The Dorian invasion and the Greek Dark Ages may thus account for a renewed influx of R1b-Z2103 lineages accompanying the dialects that would eventually help form the Hellenic Koiné. In a sense, it is only natural that demographically stronger populations around the Bronze Age Aegean would suffer a limited (male) population replacement with the succeeding invasions, starting with a higher genetic impact in the north-west and diminishing as they progressed to the south and the east, coupled with stepped admixture events with local populations.

This would be therefore the late equivalent of what happened at the end of the 3rd millennium BC, with Mycenaeans and their genetic continuity with Minoans.

Distribution of Pre-Greek place-names ending in -ssos/-ssa or -sos/-sa. See original images and more on the south/east cline distribution of Pre-Greek place-names here.

Sea peoples of hg. R1b-M269

Thanks to Wang et al. (2018) supplementary materials we knew that one of the two Levantine LBA II samples from Tel Shadud (final 13th–early 11th c. BC) published in van den Brink (2017) was of hg. R1b-M269 – in fact, the one interpreted as a Canaanite official residing at this site and emulating selected funerary aspects of Egyptian mortuary culture.

Both analyzed samples, this elite individual and a commoner of hg. J buried nearby, were genetically similar and indistinguishable from local populations, though:

Principal Components Analysis of L112 and L126 was carried out within the framework described in Lazaridis et al. (2016). This analysis showed that the two individuals cluster genetically, with similar estimated proportions of ancestry from diverse West Eurasian ancestral sources. These results are consistent with the hypothesis that they derive from the same population, or alternatively that they derive from two quite closely related populations.

We know that ancestry changes easily within a few generations, so there was not much information to go on, except for the fact that – being R1b-M269 – this individual could trace his paternal ancestor at some point to Proto-Indo-Europeans.

One might think that, because many haplogroups in this spreadsheet were wrong, this is also wrong; nevertheless, many haplogroups are correctly identified by Yleaf, and finding R1b-M269 in the Levant after the expansion of Sea Peoples could not be that surprising, because they were most likely related to populations of the Aegean Sea. Any other related hg. R1b (R1b-M73, R1b-V88, even R1b-V1636) wouldn’t fit as well as R1b-M269.


However, the early expansion of Proto-Indo-Aryans into the Middle East, as well as the later expansion of Armenians from the Balkans through Anatolia and of West Iranians from the east may have all potentially been related to this sample. But still, the previous linguistic and archaeological theories concerning the Philistines and the expansion of Sea Peoples in the Levant made this sample a likely (originally) Greek “Dorian” lineage, rather than the other (increasingly speculative) alternatives.

In any case, it was obvious to anyone – that is, to anyone with a minimum knowledge of how population genomics works – that just the two samples from van den Brink (2017) couldn’t be used to get to any conclusions about the ancestral origin of these individuals (or their differences) beyond Levantine peoples, because their ancestry was essentially (i.e. statistically) the same as the other few available ancient samples from nearby regions and similar periods.

If anything, the PCA suggested an origin of the R1b sample closer to Aegean populations relative to the J individual (see PCA above), and this should have been supported also by amateur models, without any possible confirmation (as with the ASH_IA2 cluster in this paper). However, if you have followed online discussions of Tel Shadud R1b-M269 sample since it was mentioned first on Eupedia months ago – including another wave of misguided speculation based on the ancestry of both individuals triggered by a discussion on this blog -, you have once more proof of how misleading ancestry analyses can be in the wrong hands.

NOTE. This is the Nth proof (and that only in 2019) of how it’s best to just avoid amateur analyses and interpretations altogether, as I did in the recent publication of the books. All those who didn’t take into account whatever was commented about the ancestry of these samples haven’t lost a single bit of relevant information on Levantine peoples, and have had more time for useful reads, compared to those dedicated to endless void speculation, once again gone awfully wrong, as does everything related to cocky ancient DNA crackpottery 😉

Late Bronze Age population movements in the Eastern Mediterranean and the Middle East. See full map including ancient DNA samples with Y-DNA, mtDNA, and ADMIXTURE.

Admittedly, though, even accepting the evident Mediterranean origin of this lineage, one could have argued that this sample may have been of R1b-L151 subclade, if one were inclined to support the theory that Italic peoples were behind Sea Peoples expanding east – and consequently that the ancestors of Etruscans had migrated eastward into the Aegean (e.g. into Lemnos), so that it could be asserted that Tyrsenian might have been a remnant language of an ancient population of northern Italy.


Fortunately, some of the samples recovered in Feldman et al. (2019) that could be analyzed (those of the cluster ASH_IA1) offer a very specific time frame where European ancestry appeared (ca. 1250 BC) before it subsequently became fully diluted (as seen in cluster ASH_IA2) among the prevalent Levantine ancestry of the area.

Also fortunately, this precise cluster shows another R1b-M269 sample, likely R1b-Z2103 (because it is probably xL151), and this sample together with others from the same cluster prove that the ancestry related to the original southern European incomers was:

  1. Recent, related thus to LBA population movements, as expected; and
  2. More closely related to coeval Aegeans, including Mycenaeans with Steppe-related ancestry.

NOTE. I say “fortunately” because, as you can imagine if you have dealt with amateurish discussions long enough, without this cluster with evident Aegean ancestry and the R1b-M269 (Z2103) sample precisely associated to it, some would enter again in endless comment loops created by ancestry magicians, showing how Aegean peoples were not behind Sea Peoples, or not behind Philistines, or not behind the R1b-M269 among Philistines, depending on their specific agendas.

Map of the Sea People invasions in the Aegean Sea and Eastern Mediterranean at the end of the Late Bronze Age (blue arrows).. Some of the major cities impacted by the raids are denoted with historical dates. Inland invasions are represented by purple arrows. From Kaniewski et al. (2011). Some of the major cities impacted by the raids are denoted with historical dates. Inland invasions are represented by purple arrows.

The results of the paper don’t solve the question of the exact origin of all Sea Peoples (not even that of Philistines), but it is quite clear that most of those forming this seafaring confederation must have come from sites around the Aegean Sea. This supports thus the traditional origin attributed to them, including a hint at the likely expansion of Eastern Mediterranean ancestry and lineages into the Italian Peninsula precisely from the Aegean, as some oral communications have already disclosed.

As an indirect conclusion from the findings in this paper, then, we can now more confidently support that Tyrsenian speakers most likely expanded into the Appenines and the Alps originally from a Tyrsenian-speaking LBA population from Lemnos, due to the social unrest in the whole Aegean region, and might have become heavily admixed with local Italic peoples quite quickly, as it happened with Philistines, resulting in yet another case of language expansion through (the simplistically called) elite domination.


Even more interesting than these specific findings, this paper confirms yet another hypothesis based on phylogeography, and proves once again two important starting points for ancient DNA interpretation that I have discussed extensively in this blog:

  • The rare R1b-M269 Y-chromosome lineage of Tel Shadud offered ipso facto the most relevant clue about the ancestral geographical origin of this Canaanite elite male’s paternal family, most likely from the north-west based on ancient phylogeography, which indirectly – in combination with linguistics and archaeology – supported the ancestral ethnolinguistic identification of Philistines with the Aegean and thus with (a population closest to) Ancient Greeks.
  • Ancestry analyses are often fully unreliable when assessing population movements, especially when few samples from incomplete temporal-geographical transects are assessed in isolation, because – unlike paternal (and maternal) haplogroups – ancestry might change fully within a few generations, depending on the particular anthropological setting. Their investigation is thus bound by many limitations – of design, statistical, and anthropological (i.e. archaeological and linguistic) – which are quite often not taken into account.

These cornerstones of ancient DNA interpretation have been already demonstrated to be valid not only for Levantine populations, as in this case, but also for Balkan peoples, for Bell Beakers, for steppe populations (like Khvalynsk, Sredni Stog, Yamna, Corded Ware), for Basques, for Balto-Slavs, for Ugrians and Samoyeds, and for many other prehistoric peoples.

I rest my case.


Resurge of local populations in the final Corded Ware culture period from Poland


Open access A genomic Neolithic time transect of hunter-farmer admixture in central Poland, by Fernandes et al. Scientific Reports (2018).

Interesting excerpts (emphasis mine, stylistic changes):

Most mtDNA lineages found are characteristic of the early Neolithic farmers in south-eastern and central Europe of the Starčevo-Kőrös-Criş and LBK cultures. Haplogroups N1a, T2, J, K, and V, which are found in the Neolithic BKG, TRB, GAC and Early Bronze Age samples, are part of the mitochondrial ‘Neolithic package’ (which also includes haplogroups HV, V, and W) that was introduced to Europe with farmers migrating from Anatolia at the onset of the Neolithic17,31.

A noteworthy proportion of Mesolithic haplogroup U5 is also found among the individuals of the current study. The proportion of haplogroup U5 already present in the earliest of the analysed Neolithic groups from the examined area differs from the expected pattern of diversity of mtDNA lineages based on a previous archaeological view and on the aDNA findings from the neighbouring regions which were settled by post-Linear farmers similar to BKG at that time. A large proportion of Mesolithic haplogroups in late-Danubian farmers in Kuyavia was also shown in previous studies concerning BKG samples based on mtDNA only, although these frequencies were derived on the basis of very small sample sizes.


A significant genetic influence of HG populations persisted in this region at least until the Eneolithic/Early Bronze Age period, when steppe migrants arrived to central Europe. The presence of two outliers from the middle and late phases of the BKG in Kuyavia associated with typical Neolithic burial contexts provides evidence that hunter-farmer contacts were not restricted to the final period of this culture and were marked by various episodes of interaction between two societies with distinct cultural and subsistence differences.

The identification of both mitochondrial and Y-chromosome haplogroup lineages of Mesolithic provenance (U5 and I, respectively) in the BKG support the theory that both male and female hunter-gatherers became part of these Neolithic agricultural societies, as has been reported for similar cases from the Carpathian Basin, and the Balkans. The identification of an individual with WHG affinity, dated to ca. 4300 BCE, in a Middle Neolithic context within a BKG settlement, provides direct evidence for the regional existence of HG enclaves that persisted and coexisted at least for over 1000 years, from the arrival of the LBK farmers ca. 5400 BCE until ca. 4300 BCE, in proximity with Neolithic settlements, but without admixing with their inhabitants.

Principal component analysis with modern populations greyed out on the background (top), ADMIXTURE results with K = 10 with samples from this study amplified (bottom).

The analysis of two Late Neolithic cultures, the GAC and CWC, shows that steppe ancestry was present only among the CWC individuals analysed, and that the single GAC individual had more WHG ancestry than previous local Neolithic individuals. (…) The CWC’s affinity to WHG, however, contrasts with results from published CWC individuals that identified steppe ancestry related to Yamnaya as the major contributor to the CWC genomes, while here we report also substantial contributions from WHG that could relate to the late persistence of pockets of WHG populations, as supported by the admixture results of N42 and the finding of the 4300-year-old N22 HG individual. These results agree with archaeological theories that suggest that the CWC interaction with incoming steppe cultures was complex and that it varied by region.

Some comments

About the analyzed CWC samples, it is remarkable that, even though they are somehow related to each other, they do not form a tight cluster. Also, their Y-DNA (I2a), and this:

When compared to previously published CWC data, our CWC group (not individuals) is genetically significantly closer to WHG than to steppe individuals (Z = −4.898), a result which is in contrast with those for CWC from Germany (Z = 2.336), Estonia (Z = 0.555), and Latvia (Z = 1.553).

Ancestry proportions based on qpAdm. Visual representation of the main results presented in Supplementary Table S5. Populations from this study marked with an asterisk. Values and populations in brackets show the nested model results marked in green in Supplementary Table S5.

Włodarczak (2017) talks about the CWC period in Poland after ca. 2600 BC as a time of emergence of an allochthnous population, marked by the rare graves of this area, showing infiltrations initially mainly from Lesser Poland, and later (after 2500 BC) from the western Baltic zone.

Since forest sub-Neolithic populations would have probably given more EHG to the typical CWC population, these samples support the resurge of ‘local’ pockets of GAC- or TRB-like groups with more WHG (and also Levant_Neolithic) ancestry.

The known presence of I2a2a1b lineages in GAC groups in Poland also supports this interpretation, and the subsistence of such pockets of pre-steppe-like populations is also seen with the same or similar lineages appearing in comparable ‘resurge’ events in Central Europe, e.g. in samples from the Únětice and Tumulus culture.

About the Bronze Age sample, we have at last official confirmation of haplogroup R1a1a (sadly no subclade*) at the very beginning of the Trzciniec period – in a region between western (Iwno) and eastern (Strzyżów) groups related to Mierzanowice – , which has to be put in relation with the samples from the final Trzciniec period in the Baltic published in Mittnik et al. (2018).

EDIT (8 OCT 2018): More specific subclades have been published, including a R1a-Z280 lineage for the Bronze Age sample (see spreadsheet).

This confirms the early resurge of R1a-Z645 (probably R1a-Z282) lineages at the core of the developing East European Bronze Age, a province of the European Bronze Age that emerged from evolving Bell Beaker groups in Poland.

Arrival of Bell Beakers in Poland after ca. 2400 BC, and their origin in other BBC centres (Czebreszuk and Szmyt 2011).

I don’t have any hope that the Balto-Slavic evolution through BBC Poland → Mierzanowice/Iwno → Trzciniec → Lusatian cultures is going to be confirmed any time soon, until we have a complete trail of samples to follow all the way to historic Slavs of the Prague culture. However, I do think that the current data on central-east Europe – and the recent data we are receiving from north-east Europe and the Iranian steppes, at odds with the Indo-Slavonic alternative – supports this model.

I guess that, in the end, similar to how the Yamna vs. Corded Ware question is being solved, the real route of expansion of Proto-Balto-Slavic (supposedly spoken ca. 1500-1000 BC) is probably going to be decided by the expansion of either R1a-M458 (from the west) or R1a-Z280 lineages (from the east), because the limited precision of genetic data and analyses available today are going to show ‘modern Slavic’-like populations from the whole eastern half of Europe for the past 4,000 years…


Expansion of domesticated goat echoes expansion of early farmers


New paper (behind paywall) Ancient goat genomes reveal mosaic domestication in the Fertile Crescent, by Daly et al. Science (2018) 361(6397):85-88.

Interesting excerpts (emphasis mine):

Thus, our data favor a process of Near Eastern animal domestication that is dispersed in space and time, rather than radiating from a central core (3, 11). This resonates with archaeozoological evidence for disparate early management strategies from early Anatolian, Iranian, and Levantine Neolithic sites (12, 13). Interestingly, our finding of divergent goat genomes within the Neolithic echoes genetic investigation of early farmers. Northwestern Anatolian and Iranian human Neolithic genomes are also divergent (14–16), which suggests the sharing of techniques rather than large-scale migrations of populations across Southwest Asia in the period of early domestication. Several crop plants also show evidence of parallel domestication processes in the region (17).

PCA affinity (Fig. 2), supported by qpGraph and outgroup f3 analyses, suggests that modern European goats derive from a source close to the western Neolithic; Far Eastern goats derive from early eastern Neolithic domesticates; and African goats have a contribution from the Levant, but in this case with considerable admixture from the other sources (figs. S11, S16, and S17 and tables S26 and 27). The latter may be in part a result of admixture that is discernible in the same analyses extended to ancient genomes within the Fertile Crescent after the Neolithic (figs. S18 and S19 and tables S20, S27, and S31) when the spread of metallurgy and other developments likely resulted in an expansion of inter-regional trade networks and livestock movement.

Maximumlikelihood phylogeny and geographical distributions of ancient mtDNA haplogroups. (A) A phylogeny placing ancient whole mtDNA sequences in the context of known haplogroups. Symbols denoting individuals are colored by clade membership; shape indicates archaeological period (see key). Unlabeled nodes are modern bezoar and outgroup sequence (Nubian ibex) added for reference.We define haplogroup T as the sister branch to the West Caucasian tur (9). (B and C) Geographical distributions of haplogroups show early highly structured diversity in the Neolithic period (B) followed by collapse of structure in succeeding periods (C).We delineate the tiled maps at 7250 to 6950 BP, a period >bracketing both our earliest Chalcolithic sequence (24, Mianroud) and latest Neolithic (6, Aşağı Pınar). Numbered archaeological sites also include Direkli Cave (8), Abu Ghosh (9), ‘Ain Ghazal (10), and Hovk-1 Cave (11) (table S1) (9).

Our results imply a domestication process carried out by humans in dispersed, divergent, but communicating communities across the Fertile Crescent who selected animals in early millennia, including for pigmentation, the most visible of domestic traits.


Recent Africa origin with hybridization, and back to Africa 70,000 years ago


Open access Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago, by Cabrera et al. BMC Evol Biol (2018) 18(98).

Abstract (emphasis mine):


The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.


The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.


These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.


You can also read the recent interesting open access review How did Homo sapiens evolve? by Julia Galway-Witham, Chris Stringer, Science (2018) 360:6395 1296-1298.


Agricultural origins on the Anatolian plateau


New paper (behind paywall) Agricultural origins on the Anatolian plateau, by Baird et al. PNAS (2018), published ahead of print (March 19).

Abstract (emphasis mine):

This paper explores the explanations for, and consequences of, the early appearance of food production outside the Fertile Crescent of Southwest Asia, where it originated in the 10th/9th millennia cal BC. We present evidence that cultivation appeared in Central Anatolia through adoption by indigenous foragers in the mid ninth millennium cal BC, but also demonstrate that uptake was not uniform, and that some communities chose to actively disregard cultivation. Adoption of cultivation was accompanied by experimentation with sheep/goat herding in a system of low-level food production that was integrated into foraging practices rather than used to replace them. Furthermore, rather than being a short-lived transitional state, low-level food production formed part of a subsistence strategy that lasted for several centuries, although its adoption had significant long-term social consequences for the adopting community at Boncuklu. Material continuities suggest that Boncuklu’s community was ancestral to that seen at the much larger settlement of Çatalhöyük East from 7100 cal BC, by which time a modest involvement with food production had been transformed into a major commitment to mixed farming, allowing the sustenance of a very large sedentary community. This evidence from Central Anatolia illustrates that polarized positions explaining the early spread of farming, opposing indigenous adoption to farmer colonization, are unsuited to understanding local sequences of subsistence and related social change. We go beyond identifying the mechanisms for the spread of farming by investigating the shorter- and longer-term implications of rejecting or adopting farming practices.

Map of central Anatolia showing the principal sites mentioned in the text.

Interesting excerpts:

The persistence of foraging and rejection of farming at Pınarbaşı is also worthy of further consideration. Pınarbaşı’s longevity as a settlement locale in the early Holocene appears to have been based on hunting of wild mammals, wetland exploitation, and significant focus on nut exploitation, all afforded by its ecotonal setting between the hills, plain, and wetland. Perhaps this existing diversity, including nutritious storable plant resources, was a key factor in a lack of interest in adopting cultivation. Another factor may have been a conscious desire to maintain traditional identities and long-standing distinctions with other communities, in part reflected in its particular way of life and its specific connections with particular elements in landscape, for example the almond and terebinth woodlands whose harvests underwrote the continuity of the Pınarbaşı settlement.

The variability in response to the possibilities of early food production in a relatively small geographical area demonstrated here is notable and provides an example useful in evaluating the spread of farming in other regions. It shows the possible role of indigenous foragers, the potential patchwork and diffuse nature of the spread of farming, the lack of homogeneity likely in the communities caught up in the process, the probability of significant continuities in local cultural traditions within the process, and the potentially long-term stable adaptation offered by lowlevel food production. The strength of identities linked to exploitation of particular foods and particular parts of the landscape may have been a major factor contributing to rejection or adoption of food production by indigenous foragers.

The results are also relevant for understanding the processes that underpinned the initial development of farming within the Fertile Crescent itself: that is, the region in which the wild progenitors of the Old World founder crops and stock animals are found. Recent research has rejected the notion of a core area for farming’s first appearance in southwest Asia and demonstrated that farming developed in diverse ways over the Fertile Crescent zone from the southern Levant to the Zagros, very analogous to the situation just described for Central Anatolia (2). Cultivation, herding, and domestication developed in that region, and it seems inescapable that exchange of crops and herded animals occurred between communities (2), involving a spread of farming within the Fertile Crescent, leading eventually to the Neolithic farming package that was so similar across the region and which spread into Europe (5). Central Anatolia was clearly linked to the Fertile Crescent, with significant evidence of exchange and some shared cultural traditions from at least the Epipaleolithic (22). The evidence presented here demonstrates very clearly the movement of crops between settlements and regions in early phases of the Neolithic through exchange, and thus allows us to identify episodes of crop exchange that were probably taking place within the Fertile Crescent itself, but are difficult, if not impossible, to distinguish due to the presence of crop progenitors across much of the region.

A very interesting read in combination with 14C-radiometric data and climatic conditions showing potential triggers of dispersal of Neolithic lifeways from Turkey to Southeast Europe, e.g. Dispersal of Neolithic Lifeways: Absolute Chronology and Rapid Climate Change in Central and West Anatolia, by Lee Clare & Bernhard Weninger, in The Neolithic in Turkey, Vol.6 (2014), Edited by Mehmet Özdogan, Nezih Basgelen, Peter Kuniholm.

The Late Neolithic (6600-6000 cal. BC) witnesses the rapid westward dispersal of Neolithic communities, apparently reaching the Aegean in the space of a very short time (ca. 6600 cal. BC). This process is linked to the demand of individuals, groups, and communities for less vulnerable conditions in the face of climate fluctuation associated with RCC. Coastal areas not only offered respite from more frequently occurring physical impacts (extreme winters and high drought risk) in inner Anatolia, they may also have provided refuge for weaker (more vulnerable) social groups (…).

Featured image, from the latter: “In the Early Pottery Neolithic (7000-6600 cal. BC) there occurs a clear break with precedeing (PPN) traditions, attested by abandonment and decreasing size of settlements, albeit that evidence for migration of groups westwards towards the Aegean is still ambiguous (black arrows: human migrations; white arrows: Anatolian obsidian)”

See also:

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations


Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations, by van de Loosdrecht et al. Science (2018).


North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.


We analyzed the genetic affinities of the Taforalt individ-uals by performing principal component analysis (PCA) and model-based clustering of worldwide data (Fig. 2). When pro-jected onto the top PCs of African and West Eurasian popu-lations, the Taforalt individuals form a distinct cluster in an intermediate position between present-day North Africans (e.g., Amazighes (Berbers), Mozabite and Saharawi) and East Africans (e.g., Afar, Oromo and Somali) (Fig. 2A). Consist-ently, we find that all males with sufficient nuclear DNA preservation carry Y haplogroup E1b1b1a1 (M-78; table S16). This haplogroup occurs most frequently in present-day North and East African populations (18). The closely related E1b1b1b (M-123) haplogroup has been reported for Epipaleolithic Natufians and Pre-Pottery Neolithic Levantines (“Levant_N”) (16). Unsupervised genetic clustering also suggests a connection of Taforalt to the Near East. The three major components that comprise the Taforalt genomes are maximized in early Holocene Levantines, East African hunter-gatherer Hadza from north-central Tanzania, and West Africans (K = 10; Fig. 2B). In contrast, present-day North Africans have smaller sub-Saharan African components with minimal Hadza-related contribution (Fig. 2B).

Taforalt harboring an ancestry that contains additional affinity with South, East and Central African outgroups. None of the present-day or ancient Holocene African groups serve as a good proxy for this unknown ancestry, because adding them as the third source is still insufficient to match the model to the Taforalt gene pool.

Mitochondrial consensus sequences of the Taforalt indi-viduals belong to the U6a (n = 6) and M1b (n = 1) haplogroups (15), which are mostly confined to present-day populations in North and East Africa (7). U6 and M1 have been proposed as markers for autochthonous Maghreb ancestry, which might have been originally introduced into this region by a back-to-Africa migration from West Asia (6, 7). The occurrence of both haplogroups in the Taforalt individuals proves their pre-Holocene presence in the Maghreb.
(…) the diversification of haplogroup U6a and M1 found for Taforalt is dated to ~24,000 yBP (fig. S23), which is close in time to the earliest known appearance of the Iberomaurusian in Northwest Africa (25,845-25,270 cal. yBP at Tamar Hat (26)).

A summary of the genetic profile of the Taforalt individuals. (A) The top two PCs calculated from present-day African, Near Eastern and South European individuals from 72 populations. The Taforalt individuals are projected thereon (red-colored circles). Selected present-day populations are marked by colored symbols. Labels for other populations (marked by small grey circles) are provided in fig. S8. (B) ADMIXTURE results of chosen African and Middle Eastern populations (K = 10). Ancient individuals are labeled in red color. Major ancestry components in Taforalt are maximized in early Holocene Levantines (green), West Africans (purple) and East African Hadza (brown). The ancestry component prevalent in pre-Neolithic Europeans (beige) is absent in Taforalt.

The relationships of the Iberomaurusian culture with the preceding MSA, including the local backed bladelet technologies in Northeast Africa, and the Epigravettian in southern Europe have been questioned (13). The genetic profile of Taforalt suggests substantial Natufian-related and sub-Saharan African-related ancestries (63.5% and 36.5%, respec-tively), but not additional ancestry from Epigravettian or other Upper Paleolithic European populations. Therefore, we provide genomic evidence for a Late Pleistocene connection between North Africa and the Near East, predating the Neolithic transition by at least four millennia, while rejecting a potential Epigravettian gene flow from southern Europe into northern Africa within the resolution of our data.

It seems that the Taforalt gene pool (ca. 13000-12000 BC) cannot be explained by a connection with Upper Palaeolithic Europeans, but a more archaic admixture, so the authors cannot prove a migration through the Strait of Gibraltar or Sicily.

Nevertheless, these results apparently suggest:

  • That there is no contact before ca. 12000 BC through the Strait of Gibraltar; therefore the Sicilian route I support for the migration of R1b-V88 lineages is still the most likely one.
  • That the North African connection with Natufians is quite old – for which we already had modern Y-DNA investigation – , and therefore unlikely to be related to the Afroasiatic expansion.

I am glad I had some more time this week to read at least some interesting parts of the published papers, because the information to process is becoming insanely huge…


Migration vs. Acculturation models for Aegean Neolithic in Genetics — still depending strongly on Archaeology


Recent paper in Proceedings of the Royal Society B: Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean, by Kılınç et al. (2017).


The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter–gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.

The analysis of the paper highlights two points regarding the process of Neolithisation in the Aegean, which is essential to ascertain the impact of later Indo-European migrations of Proto-Anatolian and Proto-Greek and other Palaeo-Balkan speakers(texts partially taken verbatim from the paper):

  • The observation that the two central Anatolian populations cluster together to the exclusion of Neolithic populations of south Levant or of Iran restates the conclusion that farming in central Anatolia in the PPN was established by local groups instead of immigrants, which is consistent with the described cultural continuity between central Anatolian Epipalaeolithic and Aceramic communities. This reiterates the earlier conclusion that the early Neolithisation in the primary zone was largely a process of cultural interaction instead of gene flow.
Principal component analysis (PCA) with modern and ancient genomes. The eigenvectors were calculated using 50 modern west Eurasian populations, onto which genome data from ancient individuals were projected. The gray circles highlight the four ancient gene pools of west Eurasia. Modern-day individuals are shown as gray points. In the Near East, Pre-Neolithic (Epipaleolithic/Mesolithic) and Neolithic individuals genetically cluster by geography rather than by cultural context. For instance, Neolithic individuals of Anatolia cluster to the exclusion of individuals from the Levant or Iran). In Europe, genetic clustering reflects cultural context but not geography: European early Neolithic individuals are genetically distinct from European pre-Neolithic individuals but tightly cluster with Anatolians. PPN: Pre-Pottery/Aceramic Neolithic, PN: Pottery Neolithic, Tepecik: Tepecik-Çiftlik (electronic supplementary material, table S1 lists the number of SNPs per ancient individual).
  • The realisation that there are still two possibilities regarding the question of whether Aegean Neolithisation (post-7000 cal BC) involved similar acculturation processes, or was driven by migration similar to Neolithisation in mainland Europe — a long-standing debate in Archaeology:
    1. Migration from Anatolia to the Aegean: the Aegean Neolithisation must have involved replacement of a local, WHG-related Mesolithic population by incoming easterners. Central Anatolia or south Anatolia / north Levant (of which there is no data) are potential origins of the components observed. Notably, the north Aegeans – Revenia (ca. 6438-6264 BC) and Barcın (ca. 6500-6200 BC) – show higher diversity than the central Anatolians, and the population size of Aegeans was larger than that of central Anatolians. The lack of WHG in later samples indicates that they must have been fully replaced by the eastern migrant farmers.
    2. Adoption of Neolithic elements by local foragers: Alternatively, the Aegean coast Mesolithic populations may have been part of the Anatolian-related gene pool that occupied the Aegean seaboard during the Early Holocene, in an “out-of-the-Aegean hypothesis. Following the LGM, Aegean emigrants would have dispersed into central Anatolia and established populations that eventually gave rise to the local Epipalaeolithic and later Neolithic communities, in line with the earliest direct evidence for human presence in central Anatolia ca 14 000 cal BCE
  • On the archaeological evidence (excerpt):

    Instead of a single-sourced colonization process, the Aegean Neolithization may thus have flourished upon already existing coastal and interior interaction networks connecting Aegean foragers with the Levantine and central Anatolian PPN populations, and involved multiple cultural interaction events from its early steps onward [16,20,64,74]. This wide diversity of cultural sources and the potential role of local populations in Neolithic development may set apart Aegean Neolithization from that in mainland Europe. While Mesolithic Aegean genetic data are awaited to fully resolve this issue, researchers should be aware of the possibility that the initial emergence of the Neolithic elements in the Aegean, at least in the north Aegean, involved cultural and demographic dynamics different than those in European Neolithization.

    Featured image, from the article: “Summary of the data analyzed in this study. (a) Map of west Eurasia showing the geographical locations and (b) timeline showing the time period (years BCE) of ancient individuals investigated in the study. Blue circles: individuals from pre-Neolithic context; red triangles: individuals from Neolithic contexts”.