Spread of Y. pestis, earlier than previously thought, may have caused Neolithic decline


Open access Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline, by Rascovan et al. Cell (2018)

Abstract (emphasis mine):

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

(A) Schematic representation of the trajectories and time periods (thousand years before present, kyr) of major known human migrations in Eurasia during the Neolithic and Bronze Age. The observed geographic distribution and divergence times of Y. pestis strains from the Gok2 and Bronze Age clades cannot be explained by the timings and routes of these human movements.
(B) Geographic distribution of the use of animal traction and wheeled transport across Neolithic and Bronze Age populations in Eurasia, which broadly expanded during the period of 5,500 and 5,000 BP. The expansion of these technological innovations overlaps the predicted period for the expansion of the basal Y. pestis strains.
(C) Timeline indicating the proposed key historical events that contributed to the emergence and spread of plague during the Neolithic.

We have evolved in the interpretation of the plague from 1) a Corded Ware-driven disease, to 2) a steppe disease that was spread by Yamna and Corded Ware, and now 3) a (potentially) Trypillia-driven disease that spread to the west earlier than Yamna and Corded Ware, but probably also later east and west with both.

At least it still seems that the plague and its demographic consequences were a good reason for the expansion of Indo-Europeans and Uralians into Europe, as we thought…

Featured image, from the paper: “The predicted model of early dispersion of Y. pestis during Neolithic and Bronze Age was built by integrating phylogenetic information of Y. pestis strains from this period (Figure 1E), their divergence times (Figure 3), the geographic locations, carbon dating and genotypes of the individuals, and the archaeological record. The model suggests that early Y. pestis strains likely emerged and spread from mega-settlements in Eastern Europe (built by the Trypillia Culture) into Europe and the Eurasian steppe, most likely through human interaction networks. This was facilitated by wheeled and animal-powered transports, which are schematized in the map with red lines with arrows pointing in both senses. Our model builds upon a previous model (Andrades Valtuena et al., 2017) that proposed the spread of plague to be associated with large-scale human migrations (blue line).


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


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

Interesting excerpts (emphasis mine, stylistic changes):

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

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


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

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

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

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

Some comments

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

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

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

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

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

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

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

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

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

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

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

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


Corded Ware culture origins: The Final Frontier


As you can imagine from my latest posts (on kurgan origins and on Sredni Stog), I am right now in the middle of a revision of the Corded Ware culture for my Indo-European demic diffusion model, to see if I can add something new to the draft. And, as you can see, even with ancient DNA on the table, the precise origin of the Corded Ware migrants – in spite of the imaginative efforts of the Copenhagen group to control the narrative – are still unknown.

Corded Ware origins

The main objects of study in Corded Ware origins are necessarily the region where the oldest Corded Ware vessels appeared, Lesser Poland, as well as the adjacent (traditionally considered Proto-Corded Ware regions) Volhynia, Podolia, and upper Dniester river basin. These are some relevant points, continuing where I left the Eneolithic steppe developments (following Szmyt 1999, Rassamakin 1999, Kadrow 2008, Furholt 2014):

Kadrow (2008). Cultural interactions around Carpathians at the beginnings of the 3rd millennium BC: 1 – Globular Amphora culture; 2 – Sofievka group of Trypillia culture; 3 – Funnel Beaker culture; 4 – Baden culture; 5 – Kostolac culture; 6 – Coţofeni culture; 7 – Cernavoda II culture; 8 – Yamnaya culture and Usatovo group of Trypillia culture (apud Kadrow, 2001).
  • More frequent contacts were seen ca. 3500-3000 BC, with an interaction showing multidirectional migrations of larger human groups in the centuries around 3000 BC, involving a significant part of the population of central-east Europe.
  • The easternmost area of the Funnel Beaker culture had become more Baden-like with the expansion of the Baden culture in its western area ca. 3300-2900 BC (with findings up to 2600 BC), and these younger groups with Baden features moved increasingly into the western part of Volhynia.
  • The influence of the neighbouring Trypillian culture is seen in the eastern parts of Volhynia, from ca. 3000 BC, either from a younger phase CII (cf. Troyaniv, Koshilivtsy, Brînzeni, Zhvaniets, or Vychvatintsy) or later groups (cf. Gorodsk, Kasperivtsy, Sofievka, Horodiştea-Folteşti, Usatovo).
  • In the forest-steppe zone, herding and hunting activities intensified, while agricultural traditions were preserved, as shown by the Sofievka, Kasperivtsy, and Gorodsk groups. From the end of the 4th millennium BC mobile parts of the late Trypillian populations moved to the steppe zone, absorbing more and more steppe elements; among others, cord ornamentation (in Vykhvatintsy, Troyaniv, and Gorodsk groups), pottery forms (Vykhvatintsy, which served as prototype for the Thuringian Apmphorae, dispersed along the Dniester river, too), flat burials with bodies in contracted position on the left or right side (Vykhvatintsy, reminding of Polgár culture different male-female position, and later Corded Ware burials, and also Lower Mikhailovka, under a mound without stone constructions). At the end of the Trypillia culture, its agricultural system collapsed completely.
Globular Amphorae culture „exodus” to the Danube Delta: a – Globular Amphorae culture; b – GAC (1), Gorodsk (2), Vykhvatintsy (3) and Usatovo (4) groups of Trypillia culture; c – Coţofeni culture; d – northern border of the late phase of Baden culture;red arrows – direction of Globular Amphora culture expansion; blue arrow – direction of „reflux” of Globular Amphora culture (apud Włodarczak, 2008, with changes).
  • Slash and burn techniques of agriculture – especially those practiced by Trypillian and Funnel Beaker populations – must have intensified effects of natural growth of humidity (ca. 3400-2400), increasing fluvial activities in west Ukrainian river valleys, and increasing deforestation processes, which favoured pastoralism and nomadisation of the settlement system, and a consequent change of the social structure
  • At the same time, Yamna communities expanded along the lower and central Danube to the west, while the populations of the late phase of the Baden culture took the opposite direction and reached as far as Kiev in the north-east, contributing to the culture of the Sofievka group.
  • Globular Amphora communities migrated from the north-west, from eastern Poland, towards the Danube Delta and as far as the Dnieper in the east, destroying the primary structures of the communities in the supposed cradle territories of the Corded Ware culture. These communities found refuge and conditions for further development in south-eastern margin zone of the Funnel Beaker culture territories, penetrating at first the upper parts of the loess uplands like typical Funnel Beaker sites, but on the margins of their range, and also on areas avoided by Funnel Beaker settlement agglomerations. They brought with them the so-called Thuringian amphora up to Lesser Poland, borrowed from the late Trypillian Usatovo group. This resulted in the Złota culture, which eventually gave rise to the A-Amphorae.
Map of territorial ranges of Funnel Beaker Culture (and its settlement concentrations in Lesser Poland), local Tripolyan groups and Corded Ware Culture settlements (■) at the turn of the 4th/3rd millennia BC.

In the end, we are left with this information about the oldest CWC (Furholt 2014):

  • The earliest radiocarbon-dated groups associated with the Corded Ware culture come from new single graves from Jutland in Denmark and Northern Germany, ca. 2900 BC. This Early Single Grave culture is associated with the appearance of individual graves (some time after the decline of the megalithic constructions), composed of a small round barrow and a new gender-differentiated burial practice emphasising male individuals orientated west-east (with regional exceptions), combined with the internment with new local battle-axe types (A-Axe). However, there is no single type of burial or burial custom in Corded Ware:
    • In southern Sweden the prevailing orientation is north-east – south-west, and south-north, contrary to the supposed rule male individuals are regularly deposited on their left and females on their right side.
    • In the Danish Isles and north-eastern Germany, the Final Neolithic / Single Grave Period is characterized by a majority of megalithic graves, with only some single graves from typical barrows. In south Germany, west-east and collective burials prevail, while in Switzerland no graves are found.
    • In Kujawia (south-eastern Poland), Hesse (Germany), or the Baltic, west-east orientation and gender differentiation cannot be proven statistically.
Furholt (2014). Map of the Corded Ware regions of central Europe. The dark shading indicates those regions where Corded Ware burial rituals are present regularly
  • The oldest Corded Ware vessels (the A-Amphorae, which define the A-Horizon of the CWC) come probably from the Złota (or a related) group in Lesser Poland, where a mixed archaeological culture connecting Funnel Beaker, Baden, Globular Amphorae and Corded Ware appears ca. 2900-2600 BC. No cultural (typological) break is seen between earlier Globular Amphorae and the first Corded Ware Amphorae, but rather a continuum of traits and characteristics among the recovered vessels. This strengthens the connection of Corded Ware with Globular Amphorae peoples. The A-horizon expanded thus probably from Lesser Poland ca. 2800-2600, as seen in local contexts.
  • And of course we have a third way of defining Corded Ware individuals, which is the presence of herding, and thus a transition from hunter-gatherers to agropastoralists. This is how some Baltic Late Neolithic individuals with no archaeological data have been classified as members of the Corded Ware culture: Even though no cultural remains were extracted with the two ‘outlier’ individuals, their haplogroup and ancestry point to a direct origin in or around the steppe and forest-steppe region (yes, that risks circular reasoning).
Correspondence analysis of amphorae from the Złota-graveyards reveals that there is no typological break between Globular Amphorae and Corded Ware Amphorae, including ‘Strichbündelamphorae’ (after Furholt 2008)

Corded Ware peoples in genetics

So, no clear origin of Corded Ware migrants, a lot of data pointing to intense migrations and interaction among GAC, Trypillia and the western steppe population (remember Kristiansen’s ‘long-lasting GAC-CWC connection’, now ignored to favour their Yamnaya admixture™ concept), and also three ways of defining Corded Ware culture…

Maybe genetics can help:

Ukraine Neolithic cultures – mainly from Dereivka – show haplogroups R1b-V88, R1a1, and R1b-L754 (xP297, xM269), which is similar to the haplogroup distribution found in Ukraine Mesolithic, but apparently with an expanding group marked by haplogroup I2a2a1b1 (possibly I2a2a1b1b).

The first thing that stands out about Ukraine Eneolithic samples is that only two of them can be said to be really Ukraine Eneolithic (i.e. from “Sredni Stog”-related groups):

  • I5876 (Y-DNA R1a-Z93(Y3+), mtDNA U5a2a), from Alexandria, 4045-3974 calBCE (5215±20BP, PSUAMS-2832)
  • I4110 (mtDN AJ2b1), from Dereivka, 3634-3377 calBCE (4725±25 BP, UCIAMS-186349), J2b1

The other two samples are quite late, and in fact one of them is clearly too late (maybe from the Catacomb culture):

  • I5882 (mtDNA U5a2a), from Dereivka, 3264-2929 calBCE (4420±20BP, PSUAMS-2826)
  • I3499 (Y-DNA R1b-Z2103, mtDNA T2e), from Dereivka, 2890-2696 calBCE (4195±20BP, PSUAMS-2828)

Corded Ware samples from Mittnik et al. (2018) offer very wide radiocarbon dates, so it is unclear which of them may be the oldest one. Most of them cluster closely to the older Ukraine Eneolithic sample I5876, but also to later steppe_MLBA samples i.e. Sintashta, Potapovka, and especially Srubna and Andronovo). This points to a genetic continuity from Pre-Corded Ware to Classic and late Corded Ware peoples. Therefore, much like Khvalynsk-Yamna and apparently many other Neolithic cultures, these peoples did not really admix; at least not with the male population.

File modified by me from Mittnik et al. (2018) to include the approximate position of the most common ancestral components, and an identification of potential outliers. Zoomed-in version of the European Late Neolithic and Bronze Age samples. “Principal components analysis of 1012 present-day West Eurasians (grey points, modern Baltic populations in dark grey) with 294 projected published ancient and 38 ancient North European samples introduced in this study (marked with a red outline).

Lucky for us, even though the culture remains undefined, haplogroup R1a-Z645 seems like a unifying trait, as I said long ago, so we only have to wait for more samples to trace their origin. Nevertheless, it is clear that Corded Ware may not have been as genetically homogeneous as Khvalynsk, Yamna and Yamna-related cultures, further supporting its archaeological complexity:

  • Jagodno1 and Jagodno2 (Silesia), dated ca. 2800 BC, show haplogroup G? and I/J? – compatible with an origin of CWC in common with Trypillia (which shows 3 samples of haplogroup G2a2b2a, and one E) and Ukraine Neolithic (showing the expansion of I2a2a1b1 subclades).
  • I7272, from Brandýsek (Czech Republic), dated ca. 2900-2200 BC shows haplogroup I2a2a2 (compatible with an origin in Ukraine Neolithic peoples – this haplogroup is also found in Yamna Kalmykia and in the Yamna Bulgaria outlier, i.e. late western samples from the Early Yamna culture).

NOTE. This precise subclade is only present to date in Chalcolithic samples from Iberia, which points (possibly like the Esperstedt family) to local Central European haplogroups integrated in a mixed Proto-Corded Ware population. The upper subclade I2a2a is found in Neolithic samples from Iberia, the British Isles, Hungary (Koros EN, ALPc), and also south-east European Mesolithic and Neolithic samples.

  • RISE1, from Oblaczkowo (Greater Poland), ca. 2865-2578 BC, shows haplogroup R1b1.
  • The Esperstedt family samples have been analysed as R1a-M417 (xZ645), although the supposed ‘xZ645’ has not been confirmed – not even in the risky new Y-calls from Wang et al. (2018) supplementary materials.
Network analysis based on the quantitative occurrence of Corded Ware pottery forms, pottery ornamentation styles, tools,
weapons and ornaments as stated in Table 1, based on the catalogues given in Table 2, line thickness representing similarity

Maybe this heterogeneity is a problem of better defining the culture, but from what we can see the oldest CWC regions and the unifying ‘Corded Ware province’ – formed after ca. 2700 BC by Jutland and Northern Germany, the Netherlands, Saale, Bohemia, Austria and the Upper Danube regions – are for the moment not the most genetically homogeneous groups.

Homogeneity comes later – which we may tentatively identify with the expansion of the A-horizon from the northern Dnieper-Dniester and Lesser Poland area – , as seen around the Baltic (like the Battle Axe culture) with R1a-Z283 subclades, and around Sintashta (i.e. probably Abashevo – Balanovo) with R1a-Z93 subclades, which is compatible with the late spread of different Z645 groups (and potentially a unifying language) .