R1b-L23-rich Bell Beaker-derived Italic peoples from the West vs. Etruscans from the East


New paper (behind paywall) Ancient Rome: A genetic crossroads of Europe and the Mediterranean, by Antonio et al. Science (2019).

The paper offers a lot of interesting data concerning the Roman Empire and more recent periods, but I will focus on Italic and Etruscan origins.

NOTE. I have updated prehistoric maps with Y-DNA and mtDNA data, and also the PCA of ancient Eurasian samples by period including the recently published samples, now with added sample names to find them easily by searching the PDFs.

Apennine homeland problem

The traditional question of Italic vs. Etruscan origins from a cultural-historical view* lies in the opposition of the traditional way of life during the Bronze Age as opposed to increasingly foreign influences in the Final Bronze Age, which eventually brought about a proto-urban period in the Apennine Peninsula.

* From a modern archaeological perspective, as well as from the (unrelated) nativist view, “continuity” of ancient cultures, languages, and peoples is generally assumed, so this question is a no-brainer. Seeing how population genomics has essentially supported the cultural-historical view, dismissing the concepts of unscathed genomic or linguistic continuity, we have to assume that different cultures potentially represent different languages, and that genetic shift coupled with radical cultural changes show a strong support for linguistic change, although the later Imperial Roman period is an example of how this is not necessarily the case.

Early Bronze Age cultures ca. 2200 – 1750 BC. See full maps.

A little background to the Italic vs. Etruscan homeland problem, from Forsythe (2006) (emphasis mine):

While the material culture of the Po Valley developed in response to influences from central Europe and the Aegean, peninsular Italy during the late Bronze Age lagged somewhat behind for the most part. Inhumation continued to be the funerary practice of this region. Although agriculture doubtless remained the mainstay of human subsistence, other evidence (the occupation of mountainous sites not conducive to farming, the remains of cattle, sheep, pigs, and goats, and ceramic vessels used for boiling milk and making cheese) indicates that pastoralism was also very widespread. This suggests that transhumance was already a well-established pattern of human existence. In fact, since the material culture of central and southern Italy was relatively uniform at this time, it has been conjectured that this so-called Apennine Culture of c. 1600–1100 B.C. owed its uniformity in part to the migratory pattern characteristic of ancient Italian stockbreeding.

During the first quarter of the twelfth century B.C. the Bronze-Age civilizations of the eastern Mediterranean came to an abrupt end. The royal palaces of Pylos, Tiryns, and Mycenae in mainland Greece were destroyed by violence, and the Hittite kingdom that had ruled over Asia Minor was likewise swept away. The causes and reasons for this major catastrophe have long been debated without much scholarly consensus (see Drews 1993, 33–96). Apart from the archaeological evidence indicating the violent destruction of many sites, the only ancient accounts relating to this phenomenon come from Egypt. The most important one is a text inscribed on the temple of Medinet Habu at Thebes, which accompanies carved scenes portraying the pharaoh’s military victory over a coalition of peoples who had attempted to enter the Nile Delta by land and sea.


Iron metallurgy did not reach Italy until the ninth century B.C., and even then it was two or more centuries before iron displaced bronze as the most commonly used metal. Thus, archaeologists date the beginning of the Iron Age in Italy to c. 900 B.C.; and although the Italian Bronze Age is generally assigned to the period c. 1800–1100 B.C. and is subdivided into early, middle, and late phases, the 200-year interval between the late Bronze Age and early Iron Age has been labeled the Final Bronze Age.

During this period the practice of cremation spread south of the Po Valley and is attested at numerous sites throughout the peninsula. Since this cultural tradition developed into the Villanovan Culture which prevailed in Etruria and much of the Po Valley c. 900–700 B.C., modern archaeologists have devised the term “Proto-Villanovan” to describe the cremating cultures of the Italian Final Bronze Age.

The fact that some of the earliest urnfield sites of peninsular Italy are located on the coast (e.g. Pianello in Romagna and Timmari in Apulia) is interpreted by some archaeologists as an indication that cremating people had come into Italy by sea, and that their migration was part of the larger upheaval which affected the eastern Mediterranean at the end of the Bronze Age (so Hencken 1968, 78–90). On the other hand, the same data can be explained in terms of indigenous coastal settlements adopting new cultural traits as the result of commercial interaction with foreigners. In any case, by the end of the Final Bronze Age inhumation had reemerged as the dominant funerary custom of southern Italy, but cremation continued to be an integral aspect of the Villanovan Culture of northern and much of central Italy.

Diffusion of the Villanovan culture (after M. Torelli, ed., Gli Etruschi, Milan, 2000, p. 45). Modified from The Etruscan World (2013), by Turfa.

There is a myriad of linguistic reasons why eastern foreign influences can be attributed to Indo-European (mainly Anatolian, including a hypothetic influence on Latino-Faliscan) or Tyrsenian – as well as many other less credible models – and there is ground in archaeology to support any of the linguistic models proposed, given the long-lasting complex interactions of Italy with other Mediterranean cultures.

NOTE. The lack of theoretical schemes including integral archaeological-linguistic cultural-historical models due to the radical reaction against the excesses of the early 20th century have paradoxically allowed anyone (from archaeologists or linguists to laymen) to posit infinite population movements often based on the simplest similarities in vase decoration, burial practices, or shared vocabulary.

However, recent studies in population genomics have simplified the picture of Bronze Age population movements, identifying radical changes related to population replacements as opposed to more subtle admixture events. As of today, (France Bell Beaker-like) Urnfield stands as the most likely vector of Celtic languages; NW Iberian Bell Beakers as the vector of Galaico-Lusitanian; NW Mediterranean Beakers as the most likely ancestors of Elymian; the Danish Late Neolithic as representative of expanding Proto-Germanic; or Central-East Bell Beakers of Proto-Balto-Slavic.

With this in mind, the most logical conclusion is to assume that Alpine Bell Beakers (close to the sampled Italian Beakers from Parma or from southern Germany) spread Italo-Venetic languages, which is deemed to have split in the early to mid-2nd millennium BC, with dialects found widespread from the Alps to Sicily by the early 1st millennium BC.

Therefore, the two main remaining models of Italian linguistic prehistory – with the information that we already had – were as follows, concerning Tyrsenian (the ancestor of Etruscan and Rhaetian):

  1. It is a remnant language of the Italian (or surrounding) Chalcolithic, which survived in some pockets isolated from the Bell Beaker influence;
  2. It was a foreign language that arrived and expanded at the same time as the turmoil that saw the emergence of the Sea Peoples.

NOTE. Read more on Italo-Venetic evolution and on the likely distribution of Old European and Tyrsenian in the Bronze Age.

Languages of pre-Roman Italy and nearby islands. Italo-Venetic languages surrounded with shadowed red border. I1, South Picene; I2, Umbrian; I3, Sabine; I4, Faliscan; I5, Latin; I6, Volscian and Hernican; I7, Central Italic (Marsian, Aequian, Paeligni, Marrucinian, Vestinian); I8, Oscan, Sidicini, Pre-Samnite; I9, Sicel; IE1, Venetic; IE2, North Picene; IE3, Ligurian; IE4, Elymian; IE5, Messapian; C1, Lepontic; C2, Gaulish; G1-G2-G3, Greek dialects (G1: Ionic, G2: Aeolic, G3: Doric); P1, Punic; N1, Rhaetian; N2, Etruscan; N3, Nuragic. Image modified from Davius Sanctex.


A Proto-Villanovan female from Martinsicuro in the Abruzzo coast (ca. 890 BC), of mtDNA hg. U5a2b, is the earliest mainland sample available showing foreign (i.e. not exclusively Anatolia_N ± WHG) ancestry:

Martinsicuro is a coastal site located on the border of Le Marche and Abruzzo on central Italy’s Adriatic coast. It is a proto-Villanovan village, situated on a hill above the Tronto river, dating to the late Bronze Age and Early Iron Age (…) finds from the site indicate an affinity with contemporaries in the Balkans, suggesting direct trade contacts and interaction across the Adriatic. In particular, the practice of decorating ceramics with bronze elements was shared between the Nin region in Croatia and Picene region of Italy, including Martinsicuro.

NOTE. These are just some of the models I have tried, most of them unsuccessfully. The standard errors that I get are too high, but I am not much interested in this sample that seems (based on its position in the PCA and the available qpAdm results) mostly unrelated to Italic and Etruscan ethnogenesis.

The sample clusters close to the Early Iron Age sample from Jazinka (ca. 780 BC), from the central Dalmatian onomastic region, on the east Adriatic coast opposite to Abruzzo, possibly related to the south-east Dalmatian (or Illyrian proper) onomastic region to the south. However, there is no clear boundary between hydrotoponymic regions for the Bronze Age, and it is quite close to the (possibly Venetic-related) Liburnian onomastic region to the north, so the accounts of Martinsicuro belonging to the Liburni in proto-historical times can probably be extrapolated to the Final Bronze Age.

NOTE. Based on feminine endings in -ona in the few available anthroponyms, Liburnian may have shared similarities with personal names of the Noricum province, which doesn’t seem to be related to the more recent (Celtic- or Germanic-related?) Noric language. On the other hand, anthroponyms are known to show the most recent hydrotoponymic layer of a region, so these personal names might be unrelated to the ancestral language behind place and river names.

Toponyms ending in -ona (after S. Čače 2007).


A Villanovan sample from the powerful Etruscan city-state of Veio in the Tyrrhenian coast (ca. 850 BC), to the north of Rome, shows a cluster similar to later Etruscans and some Latins. Veio features prominently in the emergence of the Etruscan society. From The Etruscan World (2013) by Turfa:

In the final phase of the Bronze Age (mid-twelfth to tenth century bc) the disposition of settlements appears to be better distributed, although they are no longer connected to the paths of the tratturi (drove roads for transhumance of flocks and herds) as they had been during the Middle Bronze Age. As evidence of the intensive exploitation of land and continuous population growth there are now known in Etruria at least 70 confirmed settlements, and several more sites with indications of at least temporary occupation. The typical town of this chronological phase generally occupies high ground or a tufa plateau of more than five hectares, isolated at the confluence of two watercourses. These small plateaus, naturally or artificially protected, are not completely built up: non-residential areas within the defenses were probably intended as collecting points for livestock or zones reserved for cultivation, land used only by certain groups, or areas designated for shelter in case of enemy attack.

Taken together, the data seem to indicate the presence of individuals or families at the head of different groups. And in the final phase of the Bronze Age, there must have begun the process that generated (at least two centuries later) a tribal society based on families and the increasingly widespread ownership of land.

In the ninth century bc the territory is divided instead into rather large districts, each belonging to a large village, divided internally into widely spaced groups of huts, and into a small number of isolated villages located in strategic positions, for which we can assume some form of dependence upon the larger settlements.

Schematic reconstruction of the birth of a proto-urban center (after P. Tamburini, II Museo
territoriale del Lago di Bolsena. Vol 1. Dalle origini alperiodo etrusco, Bolsena 2007). Modified from The Etruscan World (2013), by Turfa.

Compared to the preceding period, this type of aggregation is characterized by a higher concentration of the population. To the number of villages located mostly on inaccessible plateaus, with defensive priority assigned to the needs of agriculture, are added settlements over wide plains where the population was grouped into a single hilltop location. It is a sort of synoikistic process, so, for example, at Vulci people were gathered from the district of the Fiora and Albegna Rivers, while to Veii came the communities that inhabited the region from the Tiber River to Lake Bracciano, including the Faliscan and Capenate territories. The reference to Halesos, son of Saturn, the mythical founder of Falerii in the genealogy of Morrius the king of Veii (Servius, Commentary on Aeneid 8.285) may conceal this close relationship between Veii and the Ager Faliscus (the territory of the historical Faliscans).

The great movement of population that characterizes this period is unthinkable without political organizations that were able to impose their decisions on the individual village communities: the different groups, undoubtedly each consisting of nuclei linked by bonds of kinship, located within or outside the tufa plateaus that would be the future seats of the Etruscan city-states, have cultural links between them, also attested to by the analysis of craft production, such as to imply affiliation to the same political unit and enabling us to speak of such human concentrations as “proto-urban”.

Map of Etruria Padana. Left: From 9th to 8th century BC. Right: From 6th to 4th century BC. Dipartimento di Archeologia di Bologna. Modified from The Etruscan World (2013), by Turfa.

Italic vs. Etruscan origins

Four out of five sampled Latins show Yamnaya-derived R1b-L23 lineages, including three R1b-U152 subclades, and one hg. R1b-Z2103 (in line with the variability found among East Bell Beakers), while one from Ardea shows hg. T1a-L208. A likely Volscian (i.e. Osco-Umbrian-speaking) sample from Boville Ernica also shows hg. R1b-Z2118*, an ‘archaic’ subclade within the P312 tree. These R1b-L23 subclades are also found later during the Imperial period, although in lesser proportion compared to East Mediterranean ones.

Among Etruscans, the only male sampled shows hg. J2b-CTS6190* (formed ca. 1800 BC, TMRCA ca. 1100 BC), sharing parent haplogroup J2b-Y15058 (formed ca. 2400 BC, TMRCA ca. 1900 BC) with a Croatian MBA sample from Veliki Vanik (ca. 1580 calBCE), who also clusters close to the IA sample from Jazinka.

Given the position of Latins and Etruscans in the PCA and the likely similar admixture, it is not striking that differences are subtle. From Antonio et al. (2019):

Interestingly, although Iron Age individuals were sampled from both Etruscan (n=3) and Latin (n=6) contexts, we did not detect any significant differences between the two groups with f4 statistics in the form of f4(RMPR_Etruscan, RMPR_Latin; test population, Onge), suggesting shared origins or extensive genetic exchange between them.

On the other hand, there are 3 clear outliers among 11 Iron Age individuals, and all Iron Age samples taken together form a wide Etrurian cluster, so it seems natural to test them in groups divided geographically:

Results seem inconsistent, especially for Italic peoples, due to their wide cluster. It could be argued that the samples with ‘northern’ admixture – a Latin from Palestrina Colombella (of hg. R1b-Z56) and the Volscian sample – might represent better the Italic-speaking population before the proto-urban development of Latium, especially given the reported strong Etruscan influences among the Rutuli in Ardea, which might explain the common cluster with Etruscans and the outlier with reported ‘eastern’ admixture.

Languages of Central Italy at the beginning of Roman expansion. Image modified from original by Susana Freixeiro at Wikipedia.

It makes sense then to test for a group of Etruscans (adding the Villanovan sample) and another of Italic peoples, to distinguish between a hypothetic ancestral Italic ancestry from a Tyrrhenian one:

NOTE. Fine-tuning groups based on the position of samples in the PCA or the amount of this or that component, or – even worse – based on the good or bad fits relative to the tested populations risks breaking the rules of subgroup analysis, eventually obtaining completely useless results, so interpretations for the Italic cluster need to be taken with a pinch of salt (until more similar Italic samples are published). The lack of proper rules regarding what can and cannot be done with this combined archaeological – genomic research is already visible to some extent in genetic papers which use brute force qpAdm tests for all available sampled populations, instead of selecting those potentially ancestral to the studied groups.

Tabs are organized from ‘better’ to ‘worse’ fits. In this case, as a general guide to the spreadsheets, the first tabs (to the left) show better fits for Italic peoples, and as tabs progress to the right they show ‘better’ fits for Etruscans, until it reaches the ‘infeasible’ or otherwise bad models.

This is what can be inferred from the models:

1) Steppe ancestry: Italic peoples seem to show better fits for north-western Alpine sources, closest to Bell Beakers from France or South Germany; whereas Etruscans show a likely Transdanubian source, closest to late Bell Beakers from Hungary (excluding Steppe- and WHG-related outliers).

To see if Bell Beakers from the south-west could be related, I tried the same model as in Fernandes et al. (2019), selecting Iberian BBC samples with more Steppe ancestry – to simplify my task, I selected them according to their PCA position. In a second attempt, I tried adding those intermediate with Iberia_CA, and it shows decreasing p-values, suggesting that the most likely source is close to high Steppe-related Bell Beaker populations. In both cases, models seem worse than France or Germany Bell Beakers.

Since Celtic spread with France BBC-like Urnfield peoples, and Italic peoples appear to be also ancestrally connected to this ancestry, the most plausible explanation is that they share an origin close to the Danubian EBA culture, which would probably be easily detectable by selecting precise Bell Beaker groups from South Germany.

Hypothetic expansion of Celtic-speaking peoples during the La Tène period (source). Image used in Udolph (2009) because it reflects a homeland roughly coincident with the oldest Celtic hydrotoponymy.

2) Anatolia_Neolithic ancestry: different tests seem to show that fits for EEF-related ancestry get warmer the closer the source population selected is to North-West Anatolian farmers, in line with the apparent shift from the East Bell Beaker cluster toward the Anatolia Neolithic cluster in the PCA:

These analyses suggest that there was a renewed Anatolia_N-like contribution during the Bronze Age, older than these Iron Age populations, but later than the rebound of WHG ancestry found among Late Neolithic and Chalcolithic samples from Italy, Sicily, or Sardinia, reflected in their shift in the PCA towards the WHG cluster.

From a range of chronologically closer groups clustering near Anatolia_N, the source seems to be closest to Neolithic samples from the Peloponnese. The direct comparison of Greece_Peloponnese_N against Italy_CA in the analyses labelled “Strict” shows that the sampled Greece Late Neolithic individuals are closer to the source of Neolithic ancestry of Iron Age Etrurians than the Chalcolithic samples from Remedello, Etruria, or Sardinia.

NOTE. Most qpAdm analyses are done with a model similar to Ning et al. (2019), using Corded_Ware_Germany.SG as an outgroup instead of Italy_Villabruna, because I expected to test all models against Yamnaya, too, but in the end – due to the many potential models and my limited time – I only tested those with ‘better’ fits:

Using Yamnaya_Kalmykia as outgroup gives invariably ‘worse’ results, as expected from Bell Beaker-derived populations who are directly derived from Yamnaya, despite their potential admixture with local Corded Ware peoples through exogamy during their expansion in Central Europe. The differences between Italic and Etruscan peoples have to be looked for mainly in EEF-related contributions, not in Steppe-related populations.

Detail of the PCA of Eurasian samples, including Italian samples from Antonio et al. (2019) with the selected clusters of Italic vs. Etruscans, as well as Bell Beaker and Balkan BA and related clusters and outliers. Also marked are Peloponnese Late Neolithic (Greece_N), Minoans, Mycenaeans and Armenian BA samples. See image with better resolution.

Etruscans and Sea Peoples

The sister clade of the Etruscan branch, J2b-PH1602 (TMRCA ca. 1100 BC), seems to have spread in different directions based on its modern distribution, and their global parent clade J2b-Y15058 (TMRCA ca. 1900 BC) was previously found in Veliki Vanik. J2b-L283 appears related to Neolithic expansions through the Mediterranean, based on its higher diversity in Sardinia, although its precise origin is unclear.

Based on the modern haplogroup distribution and on the TMRCA, it can be assumed that a community spread with hg. J2b-Z38240 from somewhere close to the Balkans coinciding with the population movements of the Final Bronze Age. Whether this haplogroup’s Middle Bronze Age area, probably close to the Adriatic, was initially Indo-European-speaking or was related to a regional survival of Etruscan-speaking communities remains unclear.

Greece Late Neolithic is probably the closest available population (from those sampled to date) geographically and chronologically to the Bronze Age North-Western Anatolian region, where the Tyrsenian language family is hypothesized to have expanded from.

We only have a few Iron Age samples from Etruria, dating from a period of complex interaction in the Mediterranean – evidenced by the relatively high proportion of outliers – so it is impossible to discard the existence of some remnant Bronze Age population closer to the Adriatic – from either the Italian (Apulia?) or the Balkan coasts – expanding with the Proto-Villanovan culture and responsible for the Greece_LN-like ancestry seen among the sampled Final Bronze / Iron Age populations from central Italy.

On the other hand, taking into account the ancestry of available Italian, Sardinian and Sicilian Neolithic, Chalcolithic and Bronze Age samples, the current genetic picture suggests an expansion of a different North-West Anatolia Neolithic-related population after the arrival of Bell Beakers from the north, hence probably through the Adriatic rather than through the Tyrrhenian coast, whether the common language group formed with Lemnian had a more distant origin in Bronze Age North-West Anatolian groups or in some isolated coastal community of the Adriatic.

NOTE. Admittedly, the ancestry of the Proto-Villanovan sample seems different from that of Etruscans, although a contribution of the most likely sources for Etruscans cannot be rejected for the Proto-Villanovan individual (see ‘reciprocal’ models of admixture here). In any case, I doubt that the main ancestry of the Proto-Villanovan from Abruzzo is directly related to the population that gave rise to Etruscans, and is more likely related to recent, intense bilateral exchanges in the Adriatic between (most likely) Indo-European-speaking populations.

The distribution of violin bow fibula from thirteenth century onward showing the movement of people between northern Italy, Illyria and the Aegean, Crete, and the parallel distribution of “foreign” darksurfaced handmade pottery (based on Kasuba 2008 : abb. 15; Lis 2009 ). Modified from Kristiansen (2018).

Northern Adriatic

This Adriatic connection could in turn be linked to wider population movements of the Final Bronze Age. Proto-Villanova represents the introduction of oriental influences coinciding with the demise of the local Terramare culture (see e.g. Cremaschi et al. 2016), whereas the Villanovan culture shows partial continuity with many Proto-Villanovan settlements where Etruscan-speaking communities later emerge. From Nicolis (2013):

Founded in the LBA, the village of Frattesina extended over around 20 hectares along the ‘Po di Adria’, a palaeochannel of the Po. It experienced its greatest development between the twelfth and eleventh centuries BC, when it had a dominant economic role thanks to an extraordinary range of artisan production (metalworking, working of bone and deer horn, glass) and major commercial influence due to trading with the Italian Peninsula and the eastern Mediterranean.

This is demonstrated by the presence of exotic objects and raw materials, such as Mycenaean pottery, amber, ivory, ostrich eggs, and glass paste. For the Mycenaean sherds found in settlements in the Verona valleys and the Po delta, analysis of pottery fabrics has shown that some of them very probably come from centres in Apulia where there were Aegean craftsmen and workers, whereas others would seem to have originated on the Greek mainland (Vagnetti 1996; Vagnetti 1998; Jones et al. 2002).

Reconstruction of Acqua Fredda archaeological site, Passo del Redebus, where a group of 9 smelting furnaces has been discovered dating back to the Late Bronze Age (8-9th century BC). Image modified from Trentino Cultura.

In this context a particular system of relations seems to link one specific Alpine region with the social and economic structure of the groups settling between the Adige and the Po and the eastern Mediterranean trading system. In eastern Trentino, at Acquafredda, metallurgical production on a proto-industrial scale has been demonstrated between the end of the LBA and the FBA (twelfth–eleventh centuries BC) (Cierny 2008) (Fig. 38.3). These products must have supplied markets stretching beyond the local area, linked to the Luco/Laugen culture typical of the central Alpine environment. According to Pearce and De Guio (1999), such extensive production must have been destined for the supply of metal to other markets, first of all to other centres on the Po plain, where transactions for materials of Mediterranean origin also took place.

The picture of the Final Bronze Age of these regions, which seems to be coherent with the development of the cultural setting of the Early Iron Age, shows that the birth of the proto-urban Villanovan centres of Bologna in Emilia and Verucchio in Romagna, at the beginning of the Iron Age, seems to follow a line of continuity starting with the role played by Frattesina in the Final Bronze Age (Bietti Sestieri 2008).

Reconstruction of pan-European communication network represented by the geographical spread of archaeological objects. The network nodes represent sites that have yielded an above-average number of relevant finds. The links are direct connections between neighbouring nodes. Modified from Suchowska-Ducke (2015).


The close similarities shared by Rhaetian with the oldest Etruscan inscriptions – but not with the language of later periods, when Etruscan expanded further north – together with increased ‘foreign’ contacts in the Final Bronze Age and the ‘foreign’ ancestry of Etruscans (relative to Italian Chalcolithic and to near-by Bell Beakers) support a language split close to the Adriatic, and not long before they started using the Euboean-related Old Italic alphabet. All this is compatible with an expansion associated with the Proto-Villanovan period, possibly starting along the Po and the Adige.

From Nicolis (2013):

In this geographical context the most important morphological features are the Alps and the alluvial plain of the River Po. Since Roman times the former have always been considered a geographical limit and thus a cultural barrier. In actual fact the Alps have never really represented a barrier, but instead have played an active role in mediating between the central European and Mediterranean cultures. Some of the valleys have been used since the Mesolithic as communication routes, to establish contacts and for the exchange of materials and people over considerable distances. The discovery of Ötzi the Iceman high in the Alps in 1991 demonstrated incontrovertibly that this environment was accessible to individuals and groups from the end of the fourth millennium BC.

From the Early Neolithic period the plain of the Po Valley provided favourable conditions for the population of the area by human groups from central and eastern Europe, who found the wide flat spaces and fertile soils an ideal environment for developing agricultural techniques and animal husbandry. Lake Garda represents a very important morphological feature, benefiting among other things from a Mediterranean-type microclimate, the influence of which can already be seen in the Middle Neolithic. Situated between the plain and the mountains, the hills have always offered an alternative terrain for demographic development, equally important for the exploitation of economic and environmental resources.

As documented for previous periods, in the late and final phases of the Bronze Age the northern Adriatic coast would also seem to represent an important geographical feature, above all in terms of possible long-distance trading contacts with the Aegean and eastern Mediterranean coasts. However, the geographical and morphological characteristics and the river network in this area were very different to the way they are today, and the preferred communications routes must always have been the rivers, particularly the Po and the Adige.

Map of inscriptions of Northern Italy. In green, Rhaetian inscriptions; in Pink, Etruscan inscriptions. Arrows show potential language movements through the Po and the Adige based on the relationship between both language. Image modified from Raetica.


Although it seems superfluous at this point, finding mostly Yamnaya-derived R1b-L23 lineages among speakers of another early North-West Indo-European dialect – and also the earliest to have split into its attested dialects – gives still more support to Yamnaya steppe herders as the vector of expansion of Late PIE, and their continuity up to the Iron Age also supports the strong patrilineal ties of Indo-Europeans.

This, in turn, further supports the nature of Afanasievo as the earliest separated branch from a Late Proto-Indo-European trunk, and of Khvalynsk as the Indo-Anatolian community, while a confirmation of R1b-L23 among early Greeks (speaking the earliest attested Graeco-Aryan dialect) will indirectly confirm East Yamnaya/Poltavka as the early Proto-Indo-Iranian community.

As it often happens with genetic sampling, due to many uncontrollable factors, there is a conspicuous lack of a proper regional and chronological transect of Bell Beaker and Bronze Age samples from Italy, which makes it impossible to determine the origin of each group’s ancestral components. Even though the sampled Italian Beakers don’t seem to be the best fit for Iron Age Italic-speaking peoples from Etruria, they still might have formed part of the migration waves that eventually developed the Apennine culture together with those of prevalent West-Central European Bell Beaker ancestry.

Similarly, the visible radical change from the increasingly WHG-shifted Italian farmers up to the sampled Chalcolithic individuals, including Parma Bell Beakers, to the Anatolia_N-shifted ancestry found in Iron Age Etruscans and Latins might be related to earlier population movements associated with Middle or Late Bronze Age contacts, and not necessarily to the radical social changes seen in the Final Bronze Age. The Etruscan subclade with a likely origin in the Balkans, on the other hand, suggests recent migrations from the Adriatic into Etruria.

Middle Bronze Age cultures of Italy and its surroundings ca. 1750-1250 BC. Potential source of the Greece_N-like admixture found widespread during the Iron Age. See full maps.

Until there is more data about these ancestry changes in Italy, the Balkans, and North-West Anatolia, I prefer to leave the Tyrsenian origins up in the air, so I deleted the Lemnian -> Etruscan arrow of the map of Late Bronze Age migrations, if only because an arrival through the Tyrrhenian Sea has become much less likely. An East -> West movement is still the most likely explanation for the common Tyrsenian language, culture, and ancestry, but the only Y-DNA haplogroup available seems to have an origin closer to the Adriatic.

The recent study of Sea Peoples showed – based on the previous hypothesis of the language and culture of the Philistines – that a minority of incoming elites must have imposed the language as their genetic ancestry (including haplogroups) became diluted among a majority of local peoples. Similarly, the original genetic pool of Tyrsenian speakers might have become diluted among different groups due to their more complex social organization, similar to what happened to Italic peoples during the Imperial period.

One of the most interesting aspects proven in the paper – and strongly suspected before it – is the reflection in population genomics of the change in the social system of the Italian Peninsula during the Roman expansion, and even before it during the Etruscan polity. In fact, it was not only Romans who spread and genetically influenced other European regions, but other regions – especially the more numerous Eastern Mediterranean populations – who became incorporated into a growing Etrurian community which nevertheless managed to spread its language.

In other words, Tyrsenian spread through central and northern Italy, and Latin throughout the whole Mediterranean area and mainland Europe, not (only) through population movements, but through acculturation, in a growing international system of more complex political organizations that can be inferred for most population and language expansions since the Early Iron Age. East Mediterranean populations, Scythians and other steppe peoples, East Germanic peoples, Vikings, or North-Eastern Europeans are other clear examples known to date.


Neolithic and Bronze Age Anatolia, Urals, Fennoscandia, Italy, and Hungary (ISBA 8, 20th Sep)


I will post information on ISBA 8 sesions today as I see them on Twitter (see programme in PDF, and sessions from yesterday).

Official abstracts are listed first (emphasis mine), then reports and images and/or link to tweets. Here is the list for quick access:

Russian colonization in Yakutia

Exploring the genomic impact of colonization in north-eastern Siberia, by Seguin-Orlando et al.

Yakutia is the coldest region in the northern hemisphere, with winter record temperatures below minus 70°C. The ability of Yakut people to adapt both culturally and biologically to extremely cold temperatures has been key to their subsistence. They are believed to descend from an ancestral population, which left its original homeland in the Lake Baykal area following the Mongol expansion between the 13th and 15th centuries AD. They originally developed a semi-nomadic lifestyle, based on horse and cattle breeding, providing transportation, primary clothing material, meat, and milk. The early colonization by Russians in the first half of the 17th century AD, and their further expansion, have massively impacted indigenous populations. It led not only to massive epidemiological outbreaks, but also to an important dietary shift increasingly relying on carbohydrate-rich resources, and a profound lifestyle transition with the gradual conversion from Shamanism to Christianity and the establishment of new marriage customs. Leveraging an exceptional archaeological collection of more than a hundred of bodies excavated by MAFSO (Mission Archéologique Française en Sibérie Orientale) over the last 15 years and naturally kept frozen by the extreme cold temperatures of Yakutia, we have started to characterize the (epi)genome of indigenous individuals who lived from the 16th to the 20th century AD. Current data include the genome sequence of approximately 50 individuals that lived prior to and after Russian contact, at a coverage from 2 to 40 fold. Combined with data from archaeology and physical anthropology, as well as microbial DNA preserved in the specimens, our unique dataset is aimed at assessing the biological consequences of the social and biological changes undergone by the Yakut people following their neolithisation by Russian colons.

NOTE: For another interesting study on Yakutian tribes, see Relationships between clans and genetic kin explain cultural similarities over vast distances.

Ancient DNA from a Medieval trading centre in Northern Finland

Using ancient DNA to identify the ancestry of individuals from a Medieval trading centre in Northern Finland, by Simoes et al.

Analyzing genomic information from archaeological human remains has proved to be a powerful approach to understand human history. For the archaeological site of Ii Hamina, ancient DNA can be used to infer the ancestries of individuals buried there. Situated approximately 30 km from Oulu, in Northern Finland, Ii Hamina was an important trade place since Medieval times. The historical context indicates that the site could have been a melting pot for different cultures and people of diversified genetic backgrounds. Archaeological and osteological evidence from different individuals suggest a rich diversity. For example, stable isotope analyses indicate that freshwater and marine fish was the dominant protein source for this population. However, one individual proved to be an outlier, with a diet containing relatively more terrestrial meat or vegetables. The variety of artefacts that was found associated with several human remains also points to potential differences in religious beliefs or social status. In this study, we aimed to investigate if such variation could be attributed to different genetic ancestries. Ten of the individuals buried in Ii Hamina’s churchyard, dating to between the 15th and 17th century AD, were screened for presence of authentic ancient DNA. We retrieved genome-wide data for six of the individuals and performed downstream analysis. Data authenticity was confirmed by DNA damage patterns and low estimates of mitochondrial contamination. The relatively recent age of these human remains allows for a direct comparison to modern populations. A combination of population genetics methods was undertaken to characterize their genetic structure, and identify potential familiar relationships. We found a high diversity of mitochondrial lineages at the site. In spite of the putatively distant origin of some of the artifacts, most individuals shared a higher affinity to the present-day Finnish or Late Settlement Finnish populations. Interestingly, different methods consistently suggested that the individual with outlier isotopic values had a different genetic origin, being more closely related to reindeer herding Saami. Here we show how data from different sources, such as stable isotopes, can be intersected with ancient DNA in order to get a more comprehensive understanding of the human past.

A closer look at the bottom left corner of the poster (the left columns are probably the new samples):


Plant resources processed in HG pottery from the Upper Volga

Multiple criteria for the detection of plant resources processed in hunter-gatherer pottery vessels from the Upper Volga, Russia, by Bondetti et al.

In Northern Eurasia, the Neolithic is marked by the adoption of pottery by hunter-gatherer communities. The degree to which this is related to wider social and lifestyle changes is subject to ongoing debate and the focus of a new research programme. The use and function of early pottery by pre-agricultural societies during the 7th-5th millennia BC is of central interest to this debate. Organic residue analysis provides important information about pottery use. This approach relies on the identification and isotopic characteristics of lipid biomarkers, absorbed into the pores of the ceramic or charred deposits adhering to pottery vessel surfaces, using a combined methodology, namely GC-MS, GC-c-IRMS and EA-IRMS. However, while animal products (e.g., marine, freshwater, ruminant, porcine) have the benefit of being lipid-rich and well-characterised at the molecular and isotopic level, the identification of plant resources still suffers from a lack of specific criteria for identification. In huntergatherer contexts this problem is exacerbated by the wide range of wild, foraged plant resources that may have been potentially exploited. Here we evaluate approaches for the characterisation of terrestrial plant food in pottery through the study of pottery assemblages from Zamostje 2 and Sakhtysh 2a, two hunter-gatherer settlements located in the Upper Volga region of Russia.

GC-MS analysis of the lipids, extracted from the ceramics and charred residues by acidified methanol, suggests that pottery use was primarily oriented towards terrestrial and aquatic animal products. However, while many of the Early Neolithic vessels contain lipids distinctive of freshwater resources, triterpenoids are also present in high abundance suggesting mixing with plant products. When considering the isotopic criteria, we suggest that plants were a major commodity processed in pottery at this time. This is supported by the microscopic identification of Viburnum (Viburnum Opulus L.) berries in the charred deposits on several vessels from Zamostje.

The study of Upper Volga pottery demonstrated the importance of using a multidisciplinary approach to determine the presence of plant resources in vessels. Furthermore, this informs the selection of samples, often subject to freshwater reservoir effects, for 14C dating.

Studies on hunter-gatherer pottery – appearing in eastern Europe before Middle Eastern Neolithic pottery – may be important to understand the arrival of R1a-M17 lineages to the region before ca. 7000 BC. Or not, right now it is not very clear what happened with R1b-P297 and R1a-M17, and with WHG—EHG—ANE ancestry

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe, by Warinner et al.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH), beginning in the Eneolithic (ca. 3300-2700 BCE), profoundly transformed the genes and cultures of Europe and Central Asia. Compared to Europe, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Bronze Age khirigsuur burials from Khövsgöl, Mongolia (ca. 1380-975 BCE). Only one individual showed evidence of WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. At the same time, LCMS/ MS analysis of dental calculus provides direct protein evidence of milk consumption from Western domesticated livestock in 7 of 9 individuals. Our results show that dairy pastoralism was adopted by Bronze Age Mongolians despite minimal genetic exchange with Western steppe herders.

Detail of the images:



Early Medieval Alemannic graveyard shows diverse cultural and genetic makeup


Open access Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard, by O’Sullivan et al., Science (2018) 4(9):eaao1262

Interesting excerpts:


The Alemanni were a confederation of Germanic tribes that inhabited the eastern Upper Rhine basin and surrounding region (Fig. 1) (1). Roman ethnographers mentioned the Alemanni, but historical records from the 3rd to the 6th century CE contain no regular description of these tribes (2). The upheaval that occurred during the European Migration Period (Völkerwanderung) partly explains the interchangeability of nomenclature with the contemporaneous Suebi people of the same region and periods of geographic discontinuity in the historical record (3). This diverse nomenclature reflects centuries of interactions between Romans and other Germanic groups such as the Franks, Burgundians, Thuringians, Saxons, and Bavarians. With the defeat of the Alemanni by Clovis I of the Franks in 497 CE, Alamannia became a subsumed Duchy of the Merovingian Kingdom. This event solidified the naming of the inhabitants of this region as Alemanni (3). From the 5th to the 8th century CE, integration between the Franks and the Alemanni was reflected by changed burial practices, with households (familia) buried in richly furnished graves (Adelsgrablege) (4). The splendor of these Adelsgräber served to demonstrate the kinship structure, wealth, and status of the familia and also the power of the Franks (Personenverbandstaaten, a system of power based on personal relations rather than fixed territory). Because inclusion in familia during the Merovingian period was not necessarily based on inheritance or provenance, debate continues on the symbolism of these burial rites (5).

The 7th century CE Alemannic burial site at Niederstotzingen in southern Germany, used circa 580 to 630 CE, represents the best-preserved example of such an Alemannic Adelsgrablege. (…)


Strontium and oxygen isotope data from the enamel showed that most individuals are local rather than migrants (Table 1, table S2, and fig. S2), except for individuals 10 and 3B. (…)

Analysis of uniparental markers

mtDNA haplogroups were successfully assigned to all 13 individuals (Table 1). Notably, there are three groups of individuals that share, among the assigned positions, identical haplotypes: individuals 4, 9, and 12B in haplogroup X2b4; individuals 1 and 3A in haplogroup K1a; and individuals 2 and 5 in haplogroup K1a1b2a1a.

Most individuals belong to the R1b haplogroup (individuals 1, 3A, 3C, 6, 9, 12A, 12B, and 12C), which has the highest frequency (>70%) in modern western European populations (20). Five individuals (1, 3A, 9, 12B, and 12C) share the same marker (Z319) defining haplogroup R1b1a2a1a1c2b2b1a1 [=ISOGG R1b1a1a2a1a1c2b2b1a1a] (…) individuals 1, 3A, and 6 have R1b lineage and marker Z347 (R1b1a2a1a1c2b2b) [=ISOGG R1b1a1a2a1a1c2b2b], which belongs to the same male ancestral lineage as marker Z319 [i.e. all R1b-U106]. Individual 3B instead carries NRY haplogroup G2a2b1, which is rare in modern north, west, and east European populations (<5%), only reaching common abundance in the Caucasus (>70%), southern Europe, and the Near East (10 to 15%)

Genome-wide capture

PCA plot of Niederstotzingen individuals, modern west Eurasians, and selected ancient Europeans. Genome-wide ancient data were projected against modern west Eurasian populations. Colors on PCA indicate more general Eurasian geographic boundaries than countries: dark green, Caucasus; bright green, eastern Europe; yellow, Sardinia and Canary Islands; bright blue, Jewish diaspora; bright purple, western and central Europe; red, southern Europe; dark brown, west Asia; light purple, Spain; dark purple, Russia; pale green, Middle East; orange, North Africa. The transparent circles serve to highlight the genetic overlap between regions of interest.

Genomically, the individuals buried at Niederstotzingen can be split into two groups: Niederstotzingen North (1, 3A, 6, 9, 12B, and 12C), who have genomic signals that most resemble modern northern and eastern European populations, and Niederstotzingen South (3B and 3C), who most resemble modern-day Mediterraneans, albeit with recent common ancestry to other Europeans. Niederstotzingen North is composed of those buried with identifiable artifacts: Lombards (individual 6), Franks (individual 9), and Byzantines (individuals 3A and 12B), all of whom have strontium and oxygen isotope signals that support local provenance (fig. S2) (8). Just two individuals, 3B (Niederstotzingen South) and 10 (no sufficient autosomal data, with R1 Y-haplogroup), have nonlocal strontium isotope signals. The δ18O values suggest that individuals 10 and 3B may have originated from a higher-altitude region, possibly the Swiss-German Alpine foothills (8). Combined with the genome affinity of individual 3B to southern Europeans, these data provide direct evidence for incoming mobility at the site and for contact that went beyond exchange of grave goods (4). Familia had holdings across the Merovingian Kingdom and traveled long distances to maintain them; these holdings could have extended from northern Italy to the North Sea. Nobles displayed and accrued power by recruiting outside individuals into the household as part of their traveling retinue. Extravagant burial rites of these familia are symbolic evidence of the Frankish power systems based on people Personenverbandstaaten imposed from the 5th until the 8th century CE (4). The assignment of grave goods and the burial pattern do not follow any apparent pattern with respect to genetic origin or provenance, suggesting that relatedness and fellowship were held in equal regard at this burial.


Both kinship estimates show first-degree relatedness for pairs 1/3A, 1/6, 1/9, 3A/9, and 9/12B and second-degree relatedness for 1/12B, 3A/6, 3A/12B, and 6/9. Except for 12C, all of the Niederstotzingen North individuals are detectably and closely related. The Niederstotzingen South individuals are not detectably related to each other or any other members of the cohort. (…)

We demonstrated that five of the individuals (1, 3A, 6, 9, and 12B) were kin to at least second degree (Fig. 3 and tables S15 and S16); four of these were buried with distinguishable grave goods (discussed above and in fig. S1). These data show that at Niederstotzingen, at least in death, diverse cultural affiliations could be appropriated even within the same family across just two generations. This finding is somewhat similar to the burial of the Frankish King Childeric in the 5th century CE with a combination of Frankish and Byzantine grave goods that symbolized both his provenance and military service to the Romans (4). The burial of three unrelated individuals (3B, 3C, and 12C) in multiple graves beside the rest of the cohort would imply that this Alemannic group buried their dead based on a combination of familial ties and fellowship. One explanation could be that they were adopted as children from another region to be trained as warriors, which was a common practice at the time; these children were raised with equal regard in the familia (2, 4).

Reconstruction of first- and second-degree relatedness among all related individuals. Bold black lines and blue lines indicate first- and second-degree relatedness, respectively. Dark blue squares are identified males with age-at-death estimates years old (y.o.), mtDNA haplotypes, and NRY haplogroups. Red circles represent unidentified females that passed maternal haplotypes to their offspring. The light square represents one male infant that shares its maternal haplotype with individuals 12B and 9. N.D., not determined.


The 7th century CE burial in Niederstotzingen represents the best-preserved example of an Alemannic Adelsgrablege. The observation that burial of the remains was close to a Roman crossroads, orientated in a considered way, and associated with rich grave goods points to a noble gravesite of an Alemannic familia with external cultural influences. The high percentage of males in the burial site suggests that this site was intended for a ranked warrior group, meaning that the individuals are not representative of the population existing in 7th century CE Alemannia. The kinship estimates show that kinship structure was organized around the familia, which is defined by close association of related and unrelated individuals united for a common purpose. The apparent kinship structure is consistent with the hypothesized Personenverbandstaaten, which was a system by which Merovingian nobles enforced rule in the Duchies of Alemannia, Thuringia, Burgundy, and elsewhere. Beyond the origin of the grave goods, we show isotopic and genetic evidence for contact with communities external to the region and evidence for shared ancestry between northern and southern Europeans. This finding invites debate on the Alemannic power system that may have been highly influenced by mobility and personal relations.

Texts and images distributed under the terms of the Creative Commons Attribution-NonCommercial license.


Shared ancestry of ancient Eurasian hepatitis B virus diversity linked to Bronze Age steppe


Ancient hepatitis B viruses from the Bronze Age to the Medieval period, by Mühlemann et al., Science (2018) 557:418–423.

NOTE. You can read the PDF at Dalia Pokutta’s Academia.edu account.

Abstract (emphasis):

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10−6–1.51 × 10−5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.

Geographical distribution of analysed samples and modern genotypes. a (featured image), Distribution of modern human HBV genotypes. Genotypes relevant to this Letter are shown in colour. Coloured shapes indicate the locations of the HBV-positive samples included for further analysis. b (above this text), Locations of analysed Bronze Age samples are shown as circles and Iron Age and later samples are shown as triangles. Coloured markers indicate HBV-positive samples. Ancient genotype A samples are found in regions in which genotype D predominates today, and HBV-DA27 is of subgenotype D5 which today is found almost exclusively in India.

Interesting excerpts:

We find genotype A in south-western Russia by 4.3 ka (in samples RISE386 and RISE387) in individuals belonging to the Sintashta culture, and in a Hungarian sample (DA195) from the Scythian culture. The western Scythians are related to the Bronze Age cultures of western steppe populations2 and their shared ancestry suggests that the modern genotype A may descend from this ancient Eurasian diversity and not, as previously hypothesized, from African ancestors29,30. This is also consistent with the phylogeny (Fig. 2), as well as the fact that the three oldest ancient genotype A sequences (HBV-DA195, HBV-RISE386 and HBV-RISE387) lack the six-nucleotide insertion found in the youngest (HBV-DA119) and in all modern genotype A sequences. The ancestors of subgenotypes A1 and A3 could have been carried into Africa subsequently, via migration from western Eurasia31.

The ancient HBV genotype D sequences were all found in Central Asia. HBV-DA27, found in Kazakhstan and dated to 1.6 ka, falls basal to the modern subgenotype D5 sequences that today are found in the Paharia tribe from eastern India32. DA27 and the Paharia people in India are linked by their East Asian ancestry2,33.

Dated maximum clade credibility tree of HBV. A log-normal relaxed clock and coalescent exponential population prior were used. Grey horizontal bars indicate the 95% HPD interval of the age of the node. Larger numbers on the nodes indicate the median age and 95% HPD interval of the age (in parentheses) under a strict clock and Bayesian skyline tree prior. Clades of genotypes C (except clade C4), E, F, G and H are collapsed and shown as dots. The figure includes a possible tenth genotype, J, based on a single human isolate. Taxon names for ancient samples indicate era (BA, Bronze Age; IA, Iron Age or later), sample name, sample age in years, ISO 3166 three-letter abbreviation of country of sequence origin, and region of sequence origin. Taxon names for modern samples indicate human genotype or subgenotype or host species if non-human, GenBank accession number, sample age in years, ISO 3166 three-letter abbreviation of country of sequence origin, and region of sequence origin.

(…)Despite the age of the samples and the imperfect diagnostic test, our dataset contained a high proportion of HBV-positive individuals. The actual ancient prevalence during the Bronze Age and thereafter might have been higher, reaching or exceeding the prevalence typically found in contemporary indigenous populations5. This clearly establishes the potential of HBV as powerful proxy tool for research into human spread and interactions. The data from ancient genomes reveal aspects of complexity in HBV evolution that are not apparent when only modern sequences are considered. They show the existence of ancient HBV genotypes in locations incongruent with their present-day distribution, contradicting previously suggested geographical or temporal origins of genotypes or sub-genotypes; evidence for the creation of genotype A via recombination and the emergence of the genotype outside Africa; at least one now-extinct human genotype; ancient genotype-level localized diversity; and demonstrate that the viral substitution rate obtained from modern heterochronously sampled sequences is probably misleading. Together, these findings suggest that the difficulty in formulating a coherent theory for the origin and spread of HBV may be due to genetic evidence of an earlier evolutionary scenario being overwritten by relatively recent alterations, as has previously been suggested in the context of recombination24

See also:

On Latin, Turkic, and Celtic – likely stories of mixed societies and little genetic impact


Recent article on The Conversation, The Roman dead: new techniques are revealing just how diverse Roman Britain was, about the paper (behind paywall) A Novel Investigation into Migrant and Local Health-Statuses in the Past: A Case Study from Roman Britain, by Redfern et al. Bioarchaeology International (2018), among others.

Interesting excerpts about Roman London:

We have discovered, for example, that one middle-aged woman from the southern Mediterranean has black African ancestry. She was buried in Southwark with pottery from Kent and a fourth century local coin – her burial expresses British connections, reflecting how people’s communities and lives can be remade by migration. The people burying her may have decided to reflect her life in the city by choosing local objects, but we can’t dismiss the possibility that she may have come to London as a slave.

The evidence for Roman Britain having a diverse population only continues to grow. Bioarchaeology offers a unique and independent perspective, one based upon the people themselves. It allows us to understand more about their life stories than ever before, but requires us to be increasingly nuanced in our understanding, recognising and respecting these people’s complexities.

We already have a more or less clear idea about how little the Roman conquest may have shaped the genetic map of Europe, Africa, or the Middle East, in contrast to other previous or later migrations or conquests.

Also, on the Turkic expansion, the recent paper of Damgaard et al. (Nature 2018) stated:

In the sixth century AD, the Hunnic Empire had been broken up and dispersed as the Turkic Khaganate assumed the military and political domination of the steppes22,23. Khaganates were steppe nomad political organizations that varied in size and became dominant during this period; they can be contrasted to the previous stateless organizations of the Iron Age24. The Turkic Khaganate was eventually replaced by a number of short-lived steppe cultures25 (…).

We find evidence that elite soldiers associated with the Turkic Khaganate are genetically closer to East Asians than are the preceding Huns of the Tian Shan mountains (Supplementary Information section 3.7). We also find that one Turkic Khaganate-period nomad was a genetic outlier with pronounced European ancestries, indicating the presence of ongoing contact with Europe (…).

Analyses of Turk- and Medieval-period population clusters. a, PCA of Tian Shan Hun, Turk, Kimak, Kipchack, Karakhanid and Golden Horde, including 28 individuals analysed at 242,406 autosomal SNP positions. b, Results for model-based clustering analysis at K = 7. Here we illustrate the admixture analyses with K = 7 as it approximately identifies the major component of relevance (Anatolian/ European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry).”

These results suggest that Turkic cultural customs were imposed by an East Asian minority elite onto central steppe nomad populations, resulting in a small detectable increase in East Asian ancestry. However, we also find that steppe nomad ancestry in this period was extremely heterogeneous, with several individuals being genetically distributed at the extremes of the first principal component (Fig. 2) separating Eastern and Western descent. On the basis of this notable heterogeneity, we suggest that during the Medieval period steppe populations were exposed to gradual admixture from the east, while interacting with incoming West Eurasians. The strong variation is a direct window into ongoing admixture processes and the multi-ethnic cultural organization of this period.

We already knew that the expansion of the La Tène culture, associated with the expansion of Celtic languages throughout Europe, was probably not accompanied by massive migrations (from the IEDM, 3rd ed.):

The Mainz research project of bio-archaeometric identification of mobility has not proven to date a mass migration of Celtic peoples in central Europe ca. 4th-3rd centuries BC, i.e. precisely in a period where textual evidence informs of large migratory movements (Scheeres 2014). La Tène material culture points to far-reaching inter-regional contacts and cultural transfers (Burmeister 2016).

Also, from the latest paper on Y-chromosome bottleneck:

[The hypothesis of patrilineal kin group competition] has an added benefit in that it could explain the temporal placement of the bottleneck if competition between patrilineal kin groups was the main form of intergroup competition for a limited episode of time after the Neolithic transition. Anthropologists have repeatedly noted that the political salience of unilineal descent groups is greatest in societies of ‘intermediate social scale’ (Korotayev47 and its citations on p. 2), which tend to be post-Neolithic small-scale societies that are acephalous, i.e. without hierarchical institutions48. Corporate kin groups tend to be absent altogether among mobile hunter gatherers with few defensible resource sites or little property (Kelly49 pp. 64–73), or in societies utilizing relatively unoccupied and under-exploited resource landscapes (Earle and Johnson50 pp. 157–171). Once they emerge, complex societies, such as chiefdoms and states, tend to supervene the patrilineal kin group as the unit of intergroup competition, and while they may not eradicate them altogether as sub-polity-level social identities, warfare between such kin groups is suppressed very effectively51,52.These factors restrict the social phenomena responsible for the bottleneck to the period after the initial Neolithic but before the emergence of complex societies, which would place the bottleneck-generating mechanisms in the right period of time for each region of the Old World.

Diachronic map of Late Copper Age migrations including Classical Bell Beaker (east group) expansion from central Europe ca. 2600-2250 BC

However, I recently read in a forum for linguists that the expansion of East Bell Beakers overwhelmingly of R1b-L21 subclades in the British Isles “poses a problem”, in that it should be identified with a Celtic expansion earlier than traditionally assumed…

That interpretation would be in line with the simplistic maps we are seeing right now for Bell Beakers (see below for the Copenhagen group).

If anything, the results of Bell Beaker expansions (taken alone) would seem to support a model similar to Cunliffe & Koch‘s hypotheses of a rather early Celtic expansion into Great Britain and Iberia from the Atlantic.

Spread of Indo-European languages (by the Copenhagen group).

But it doesn’t. Mallory already explained why in Cunliffe & Koch’s series Celtic from the West: the Bell Beaker expansion is too early for that; even for Italo-Celtic. It should correspond to North-West Indo-European speakers.

Not every population movement that is genetically very significant needs to be significant for the languages attested much later in the region.

This should be obvious to everyone with the many examples we already have. One of the least controversial now would probably be the expansion of R1b-DF27, widespread in Iberia probably at roughly the same time as R1b-L21 was in Great Britain, and still pre-Roman Iberians showed a mix of non-Indo-European languages, non-Celtic languages (at least Galaico-Lusitanian), and also some (certain) Celtic languages. And modern Iberians speak Romance languages, without much genetic impact from the Romans, either…

It is well-established in Academia that the expansion of La Tène is culturally associated with the spread of Celtic languages in Europe, including the British Isles and Iberia. While modern maps of U152 distribution may correspond to the migration of early Celts (or Italo-Celtic speakers) with Urnfield/Hallstatt, the great Celtic expansion across Europe need not show a genetic influence greater than or even equal to that of previous prehistoric migrations.

Post-Bell-Beaker Europe, after ca. 2200 BC.

You can see in these de novo models the same kind of invented theoretical ‘problem’ (as Iosif Lazaridis puts it) that we have seen with the Corded Ware showing steppe ancestry, with Old Hittite samples not showing EHG ancestry, or with CHG ancestry appearing north of the Caucasus but no EHG to the south.

However you may want to explain all these errors in scientific terms (selection bias, under-coverage, over-coverage, faulty statistical methods, etc.), these interpretations were simply fruit of the lack of knowledge of the anthropological disciplines at play.

Let’s hope the future paper on Celtic expansion takes this into consideration.


Phylogeny of leprosy, relevant for prehistoric Eurasian contacts


Some interesting studies were published at roughly the same time as Damgaard et al. (Nature 2018 and Science 2018), and that’s probably why they got little attention (at least by me).

Monica H. Green (also in Academia.edu), specialized in History of Medicine, summed up their relevance in Twitter quite well (her text is edited here for clarity):

I’ve been disappointed that three recent exceptional studies of one of the world’s most historically important diseases, leprosy, have gotten so little notice from the science communication. It will take me a few hours to lay out their significance. But I think it’s important to do so.

So, here are the new studies on historical distribution and evolutionary development of Mycobacterium leprae, one of two organisms that causes leprosy (fourth study dropped yesterday!).

  1. Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae, by Benjak et al., Nature Communications (2018) 9:352.
  2. Abstract:

    Leprosy is a chronic human disease caused by the yet-uncultured pathogen Mycobacterium leprae. Although readily curable with multidrug therapy (MDT), over 200,000 new cases are still reported annually. Here, we obtain M. leprae genome sequences from DNA extracted directly from patients’ skin biopsies using a customized protocol. Comparative and phylogenetic analysis of 154 genomes from 25 countries provides insight into evolution and antimicrobial resistance, uncovering lineages and phylogeographic trends, with the most ancestral strains linked to the Far East. In addition to known MDT-resistance mutations, we detect other mutations associated with antibiotic resistance, and retrace a potential stepwise emergence of extensive drug resistance in the pre-MDT era. Some of the previously undescribed mutations occur in genes that are apparently subject to positive selection, and two of these (ribD, fadD9) are restricted to drug-resistant strains. Finally, nonsense mutations in the nth excision repair gene are associated with greater sequence diversity and drug resistance.

  3. Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans, by Krause-Kyora et al., Nature Communications (2018) 9:1569
  4. NOTE. I referred to this study in this blog.

  5. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe, by Schuenemann et al., PLOS Pathogens (2018)
  6. Abstract:

    Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom—a skeleton from the Great Chesterford cemetery with a calibrated age of 415–545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

  7. The genome sequence of a SNP type 3K strain of Mycobacterium leprae isolated from a seventh‐century Hungarian case of lepromatous leprosy, by Mendum et al., International Journal of Osteoarchaeology (2018).
  8. Abstract:

    We report on a Mycobacterium leprae genome isolated from the remains of an individual with lepromatous leprosy that were excavated from a seventh‐century Hungarian cemetery. We determined that the genome was from a single nucleotide polymorphism (SNP) type 3K0 M. leprae strain, a lineage that diverged early from other M. leprae lineages. This is one of the earliest 3K0 M. leprae genomes to be sequenced to date. A number of novel SNPs as well as SNPs characteristic of the 3K0 lineage were confirmed by conventional polymerase chain reaction and Sanger sequencing. Recovery of accompanying human DNA from the burial was poor, particularly when compared with that of the pathogen. Modern 3K0 M. leprae strains have only been isolated from East Asia and the Pacific, and so these findings require new scenarios to describe the origins and routes of dissemination of leprosy during antiquity that have resulted in the modern phylogeographical distribution of M. leprae.

A fifth study can be added to the list, which, though not as extensive, is significant because it validates findings of others: Mycobacterium leprae genomes from naturally infected nonhuman primates, by Honap et al. PLOS Neglected Tropical Diseases (2018).


Leprosy is caused by the bacterial pathogens Mycobacterium leprae and Mycobacterium lepromatosis. Apart from humans, animals such as nine-banded armadillos in the Americas and red squirrels in the British Isles are naturally infected with M. leprae. Natural leprosy has also been reported in certain nonhuman primates, but it is not known whether these occurrences are due to incidental infections by human M. leprae strains or by M. leprae strains specific to nonhuman primates. In this study, complete M. leprae genomes from three naturally infected nonhuman primates (a chimpanzee from Sierra Leone, a sooty mangabey from West Africa, and a cynomolgus macaque from The Philippines) were sequenced. Phylogenetic analyses showed that the cynomolgus macaque M. leprae strain is most closely related to a human M. leprae strain from New Caledonia, whereas the chimpanzee and sooty mangabey M. leprae strains belong to a human M. leprae lineage commonly found in West Africa. Additionally, samples from ring-tailed lemurs from the Bezà Mahafaly Special Reserve, Madagascar, and chimpanzees from Ngogo, Kibale National Park, Uganda, were screened using quantitative PCR assays, to assess the prevalence of M. leprae in wild nonhuman primates. However, these samples did not show evidence of M. leprae infection. Overall, this study adds genomic data for nonhuman primate M. leprae strains to the existing M. leprae literature and finds that this pathogen can be transmitted from humans to nonhuman primates as well as between nonhuman primate species. While the prevalence of natural leprosy in nonhuman primates is likely low, nevertheless, future studies should continue to explore the prevalence of leprosy-causing pathogens in the wild.

These five studies are doing whole-genome sequencing on either modern isolates of M. leprae, or genomic fragments retrieved from buried remains (aDNA). The main objective of all the studies is to understand the diversity of M. leprae, both in terms of its history and in terms of its present-day distribution. (Benjak et al. 2018 are especially concerned to study possible reasons for variance in multiple drug resistance).

The following comments are concerned only to discuss leprosy’s history.

So, let’s start with a common claim of the science communication pieces on Schuenemann et al. 2018, which was published last week. A common formula: “New Study Suggests Leprosy Began To Spread From Europe To The World“. Is it plausible that Europe was where leprosy originated as human disease?

The answer, actually, is no. There’s two reasons for this, one having to do with chronology, the other with geography.

For chronology, these studies cumulatively suggest we are looking at a bottleneck. The current Time to Most Recent Common Ancestor (TMRCA) suggested for the divergence of M. leprae from its closest known “cousin,” M. lepromatosis (which also causes leprosy in humans) is estimated to be ca. 13.9 million years. There were no humans around 13.9M ya. So we cannot have been M. leprae‘s original host. All studies being discussed here agree on a consensus phylogeny, which puts the origin of all known strains of M. leprae at about 4-5K ya. So when we talk about the “origin” of M. leprae, we only talking about those lineages formed after this bottleneck.

Next we have to look at geography. Let’s start with this statement from the most recent study, Mendum et al. 2018, which is discussing a genome sequenced from an individual in Hungary from the 7th c. CE: “Modern 3K0 M. leprae strains have only been isolated from East Asia and the Pacific and so these findings require new scenarios to describe the origins and routes of dissemination of leprosy during antiquity that have resulted in the modern phylogeographical distribution of M. leprae.”

Okay, so stop and consider the implications of this. We have someone from 7th c. Hungary with leprosy. The strain of M. leprae that he has is not most closely related to strains sequenced earlier in Denmark or Sweden or England (see Schuenemann et al. 2018, refs. 9, 20, & 21). Rather, the strain he has (3K0) is most closely related to modern strains currently documented on the Pacific Rim, a very, very long way from Hungary. Here are the summary reflections of Mendum et al. 2018:

The global distribution of 3K0 and 3K1 strains is today restricted to regions of the Western Pacific such as Japan (except Okinawa), Korea, China, The Philippines, New Caledonia and Indonesia amongst others (Kai et al, 2013; Avanzi et al, 2015; Monot el al, 2009; Weng et al, 2013; Honap et al, 2018). This could indicate that the 3K lineage originated in Northern or Eastern Asia. The presence of two type 3K cases (KD271 and 222) in early medieval Hungary would then suggest a route of dissemination from Asia to central Europe, perhaps via trade links or migrations. This would be consistent with what is known of the origins of the Pannonian Avars, who are believed to have reached the Hungarian plain from the Eurasian steppe in the late 6th to early 9th centuries (Curta, 2006). The other possibility is that Europe was a centre of dissemination of the ancestral 3K0 and related strains, some of which later became less common or even absent from Europe but persisted in East Asia and the Pacific. Determining the likelihood of each of these scenarios will require more sampling and characterisation of both ancient and modern strains.

Two things bear stressing:

  1. The lineage in which the Hungarian sample has been placed, Lineage 0, has now been documented in historical remains from Denmark, too. (Schuenemann et al. 2018) So whatever transmission routes are postulated to connect the Pacific Rim to Hungary, we will also need to postulate routes to connect the Pacific Rim to Denmark.
  2. Schuenemann et al. 2018 document four of the five known M. leprae lineages in medieval western Europe. (Mendum et al. 2018 now declare the existence of 6 lineages; see tree.)
Phylogenetic relationships between selected modern (regular text) and ancient (bold text) M. leprae strains. The phylogeny was inferred by the Maximum Likelihood method of MEGA7 (Kumar et al, 2016) and the Tamura-3-Parameter model. The tree with the highest log likelihood value is shown. Bootstrap percentages from 1000 replicates are shown next to the branches. The scale indicates the number of substitutions per site. All positions with less than 90% site coverage were eliminated. M. lepromatosis was used as an outgroup (not shown). CM1 and Br15-1 are derived from a cynomolgus macaque and a red squirrel respectively.

Now, remember that we also need to keep chronology in mind: Lineage 0 is thought to have diverged from the common ancestor of Lineages 1-4 at least 3.5K ya. (Here’s the phylogenetic tree from Benjak et al. 2018, which I have marked with time divisions for emphasis.)

Modified image by Monica H. Green. Phylogeny of M. leprae. Bayesian phylogenetic tree of 146 genomes of M. leprae calculated with BEAST 2.4.4. Hypermutated samples with mutations in the nth gene were excluded from the analysis. The tree is drawn to scale, with branch lengths representing years of age. Samples were binned according to geographic origin as given in the legend. Posterior probabilities for each node are shown in gray. Location probabilities of nodes were inferred by the Discrete Phylogeny model

So what we need to explain is how a strain (Lineage 0, or 3K0 as Mendum et al. 2018 call it) can be found all the way from Denmark to New Caledonia. An “Out of Europe” narrative isn’t really helpful, any more than the earlier “Out of Africa” narrative worked.

Given the extreme amount of suffering leprosy has caused, and continues to cause around the world, and given the extraordinary investigative power that paleogenetics has now developed, it’s really time that we did a better job pulling these global narratives together.

If you have Twitter, be sure to retweet this thread!

NOTE. Another (probably also interesting) article was published recently, Digging up the plague: A diachronic comparison of aDNA confirmed plague burials and associated burial customs in Germany, by Gutsmiedl-Schümann, Praehistorische Zeitschrift (2018) 92:2, but sadly my university does not have access to it.


Plague outbreaks in the past are mainly known from written sources; in particular, the Justinianic Plague of the Early Middle Ages and the Black Death of the Late Middle Ages have been described in vivid detail. Yet prior to the introduction of aDNA analysis, it was often quite difficult to associate burials with plague beyond doubt – especially in areas where written evidence of the plague is scarce. As analysis of ancient DNA now allows the detection of plague victims in the archaeological record, new ways are being developed for combining archaeological, historical and ancient DNA research. In this paper we would like to present and compare known examples of plague graves from the Early Middle Ages, the Late Middle Ages and the Thirty Years’ War in Germany that have also been confirmed by ancient DNA analyses. We would like to argue for a differentiated view of the burial customs, especially when more than one plague victim shared a grave, and would like to show possible conclusions, drawn from the aDNA-confirmed plague burials, that can indicate the different strategies adopted by ancient societies to deal with catastrophic events like a pandemic disease.


Tracking material cultures with ancient DNA: medieval Norse walrus ivory trade, and leather shields from Zanzibar


Two papers have been recently published, offering another interesting use of ancient DNA analysis for Archaeology and, potentially, Linguistics.

Open access Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland, by Star, Barrett, Gondek, & Boessenkool, bioRxiv (2018).

Abstract (emphasis mine):

The search for walruses as a source of ivory -a popular material for making luxury art objects in medieval Europe- played a key role in the historic Scandinavian expansion throughout the Arctic region. Most notably, the colonization, peak and collapse of the medieval Norse colony of Greenland have all been attributed to the proto-globalization of ivory trade. Nevertheless, no studies have directly traced European ivory back to distinct populations of walrus in the Arctic. This limits our understanding of how ivory trade impacted the sustainability of northern societies and the ecology of the species they relied on. Here, we compare the mitogenomes of 27 archaeological walrus specimens from Europe and Greenland (most dated between 900 and 1400 CE) and 10 specimens from Svalbard (dated to the 18th and 19th centuries CE) to partial mitochondrial (MT) data of over 300 modern walruses. We discover two monophyletic mitochondrial clades, one of which is exclusively found in walrus populations of western Greenland and the Canadian Arctic. Investigating the chronology of these clades in our European archaeological remains, we identify a significant shift in resource use from predominantly eastern sources towards a near exclusive representation of walruses from western Greenland. These results provide empirical evidence for the economic importance of walrus for the Norse Greenland settlements and the integration of this remote, western Arctic resource into a medieval pan-European trade network.

(A) Population distribution, historic trade routes and sample locations of Atlantic walrus in the northern Atlantic region. The range of modern Atlantic walrus (dark grey) and putative dispersal routes (black arrows) follow (58) and (31). Eight breeding populations are recognized (58); 1 – Foxe Basin, 2 – Hudson Bay, 3 – Hudson Strait, 4, – West Greenland, 5 – North Water, 6 – East Greenland, 7 – Svalbard/Franz Josef land, 8 – Novaya Zemlya. Historic trade routes from Greenland –including the location of Norse settlements– and northern Fennoscandia/Russia (yellow) indicate possible sources from which walrus ivory was exported to Europe during the Middle Ages. The Svalbard specimens (orange) were originally from hunting stations of the 1700s and 1800s. The other Atlantic walrus specimens (red, grey) were obtained from museum collections. (B) Bayesian phylogenetic tree obtained using BEAST (84) based on 346 mitochondrial SNPs using Pacific walrus (PAC) as an outgroup. Numbers represent the different specimens as listed in Table S1, and colors match the sampling locations as in Fig. 1A. Branches with a posterior probability of one (grey circles) are indicated. (C) Distribution of RFLP and control region (CR) haplotypes of modern Atlantic walrus populations. The RFLP clade classification follows Born, Andersen et al. (2001). The distribution of a distinct ACC CR haplotype is from 306 modern specimens (see material and methods).

Determination of the geographical origin of leather shields from Zanzibar using ancient DNA tools, by Bastian, Jacot-des-Combes, Hänni, & Perrier, J Arch. Sci (2018) 19:323-333.


Zanzibar shields are documented in several books and preserved in many European, African and Omani museums. They are relatively small and decorated; therefore, we can assume that they served to not only to protect the hand during sword combat but also to attract the attention of the attacker. As with all shields, they are also an object of prestige and armorial bearing to identify the owner’s army corps. Within the incredible cultural and ethnic mosaic of this part of the Indian Ocean, the shield enables alliances, protection systems and allegiance to be specified and clarified.

This study is a step towards understanding the nature of the relationships between Oman and the various communities living on the western coast of the Indian Ocean based on their material culture, especially their shields. Identifying the animal species used to make the shields was crucial in establishing both the manufacturers and the consumers of these objects. DNA analyses indicated that the leather used for the studied Zanzibar shields is rhinoceros (Diceros bicornis michaeli); a subspecies historically only present on the coast of East Africa. Our results also indicate that the shields, used mainly in Oman, Zanzibar and other regions with a strong relationship with Oman power, were made in Zanzibar and the Arabian Peninsula.

Ancient distribution of Diceros bicornis michaeli (eastern black rhinoceros) from southern Sudan, Ethiopia, and Somalia through Kenya into northern-central Tanzania. Dark grey represents the presence of both species. At the tip of the arrow: Zanzibar Island. Copyright: Fabiola Bastian.

In a time when many geneticists seem to have shifted their full attention to novel statistical methods applied to a few ancient individuals, it feels good to see some of them using their research to complement traditional academic disciplines instead.

This kind of studies may help track with more detail the most obvious harbinger of potential prehistoric language change: the diffusion of material culture.

See also:

The time and place of European admixture in Ashkenazi Jewish history

Open access The time and place of European admixture in Ashkenazi Jewish history, by Xue, Lencz, Darvasi, Pe’er, & Carmi, PLOS Genetics (2018).

Abstract (emphasis mine):

The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60–80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25–50 generations ago.

Principal Component Analysis (PCA) of the European and Middle-Eastern samples used as reference panels in our study. The analysis was performed using SmartPCA [25] with default parameters (except no outlier removal). The populations included within each region are listed in Table 1 of the main text. The PCA plot supports the partitioning of the European and Middle-Eastern populations into the broad regional groups used in the analysis. https://doi.org/10.1371/journal.pgen.1006644.s001

Interesting excerpts:

(…) AJ genetics defies simple demographic theories. Hypotheses such as a wholly Khazar, Turkish, or Middle-Eastern origin have been disqualified [4–7, 17, 55], but even a model of a single Middle-Eastern and European admixture event cannot account for all of our observations. The actual admixture history might have been highly complex, including multiple geographic sources and admixture events. Moreover, due to the genetic similarity and complex history of the European populations involved (particularly in Southern Europe [51]), the multiple paths of AJ migration across Europe [10], and the strong genetic drift experienced by AJ in the late Middle Ages [9, 16], there seems to be a limit on the resolution to which the AJ admixture history can be reconstructed.

A proposed model for the recent AJ history. The proposed intervals for the dates and admixture proportions are based on multiple methods, as described in the main text. https://doi.org/10.1371/journal.pgen.1006644.g007

Historical model and interpretation

Under our model, admixture in Europe first happened in Southern Europe, and was followed by a founder event and a minor admixture event (likely) in Eastern Europe. Admixture in Southern Europe possibly occurred in Italy, given the continued presence of Jews there and the proposed Italian source of the early Rhineland Ashkenazi communities [3]. What is perhaps surprising is the timing of the Southern European admixture to ≈24–49 generations ago, since Jews are known to have resided in Italy already since antiquity. This result would imply no gene flow between Jews and local Italian populations almost until the turn of the millennium, either due to endogamy, or because the group that eventually gave rise to contemporary Ashkenazi Jews did not reside in Southern Europe until that time. More detailed and/or alternative interpretations are left for future studies.

Recent admixture in Northern Europe (Western or Eastern) is consistent with the presence of Ashkenazi Jews in the Rhineland since the 10th century and in Poland since the 13th century. Evidence from the IBD analysis suggests that Eastern European admixture is more likely; however, the results are not decisive. An open question in AJ history is the source of migration to Poland in late Medieval times; various speculations have been proposed, including Western and Central Europe [2, 10]. The uncertainty on whether gene flow from Western Europeans did or did not occur leaves this question open.

The effect of gene flow from the Middle-East into Southern EU on f4 statistics. Panels (A) and (B) demonstrate f4(West-EU,YRI;AJ,ME) and f4(South-EU,YRI;AJ,ME), respectively (cf S4A Fig). Paths from the Middle-East into AJ are indicated with red arrows; paths from YRI to Western or Southern Europe with green arrows. The f4 statistic is proportional to the total overlap between these paths (black bars). Whereas panel (B) (f4(South-EU,YRI;AJ,ME)) has more overlapping branches than in (A), migration from the Middle-East into Southern EU introduces a branch where the arrows run in opposite directions (patterned bar). Hence, the observed f4 statistic in (B) may be lower (depending on branch lengths) than in (A), even if Southern EU is the true source of gene flow into AJ. https://doi.org/10.1371/journal.pgen.1006644.s005

Featured image: Expulsions of Jews, from Wikipedia.