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

spread-yersinia-pestis

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.

spread-yersinia-trypillia
(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).

Related

Eastern pressure blade technology in west Scandinavia associated with WHG

New interesting preprint Ancient DNA from chewing gums connects material culture and genetics of Mesolithic hunter-gatherers in Scandinavia, by Kashuba et al. (2018).

Interesting excerpts (emphasis mine):

Mitochondrial genomes from all three individuals belong to the U5a2d haplogroup. (…) The mitochondrial U5a2d haplogroup is consistent with earlier published results for ancient individuals from Scandinavia, U5a being the most common within SHG. Of the 16 Mesolithic individuals from Scandinavia published prior to our study, seven belong to the U5a haplogroup, nine share the U2 and U4 haplogroups

We divided the SHG group into two groups: SHGa and SHGb (ancient individuals found in contemporary Norway and Sweden, respectively). We based this on both the geographical distribution and the previous studies demonstrating the close relation of SHGa to EHG group and SHGb to WHG group. To further explore the demography within the SHG group, we compared the ancestry of BLE individuals within SHGa and SHGb groups. This comparison revealed a high relative shared drift between BLE individuals and the SHGb group

scandinavia-hunter-gatherer-admixture
Admixture analysis showing the major mode for K=15. The figure represents 11 runs out of 20 replicates (Greedy algorithm ran with the Jaccard distance and a 0.97 similarity threshold)

The results from Huseby Kiev allow us to finally connect the SHG group with the eastern pressure blade technology. However, the higher genetic affinity between Huseby Kiev individuals and the WHG group challenges the earlier suggested tie between eastern technology and EHG genetics. Our results suggest either early cultural transmission, or a more complex course of events involving both non- and co-dependent cultural and genetic admixture.

huseby-kiev

Seeing how culture is indeed usually associated with the expansion of a certain population, especially at such an early date, I guess this similarity with WHG of incoming eastern peoples comes from an originally EHG population expanding into a mainly WHG area in the west (similar to what happens e.g. with Bell Beakers), or being replaced later by a WHG population which adopted the culture (similar to what happened with late Corded Ware populations in central-east Europe after the expansion of Bell Beakers).

Unlike later periods, it will always be difficult to judge such ancient population movements with few samples covering thousands of years… Probably specific Y-DNA haplogroups would help differentiate between both expanding populations from east and west.

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Biparental inheritance of mitochondrial DNA in humans

mtdna-inheritance-paternal

New paper Biparental Inheritance of Mitochondrial DNA in Humans, by Luo et al. PNAS (2018).

Interesting excerpts (emphasis mine):

Abstract

Although there has been considerable debate about whether paternal mitochondrial DNA (mtDNA) transmission may coexist with maternal transmission of mtDNA, it is generally believed that mitochondria and mtDNA are exclusively maternally inherited in humans. Here, we identified three unrelated multigeneration families with a high level of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals. Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA sequencing analysis in our research laboratory and in two Clinical Laboratory Improvement Amendments and College of American Pathologists-accredited laboratories using multiple approaches. A comprehensive exploration of mtDNA segregation in these families shows biparental mtDNA transmission with an autosomal dominantlike inheritance mode. Our results suggest that, although the central dogma of maternal inheritance of mtDNA remains valid, there are some exceptional cases where paternal mtDNA could be passed to the offspring. Elucidating the molecular mechanism for this unusual mode of inheritance will provide new insights into how mtDNA is passed on from parent tooffspring and may even lead to the development of new avenues for the therapeutic treatment for pathogenic mtDNA transmission.

An example

Compared with Family A, a strikingly similar mtDNA transmission pattern was demonstrated in Families B and C. Taking Family B for illustration, II-3 having 29 heteroplasmic and seven homoplasmic variants should have inherited mtDNA from both his father (I-1, haplogroup of K1b2a) and his mother (I-10, haplogroup of H), who were supposed to possess 34 and nine homoplasmic variants, respectively. II-3 further transmitted his mtDNA that he inherited from I-1 to his son (III-2), who also inherited all of his mother’s mtDNA (II-30, carrying 34 variants and a haplogroup of T2a1a). However, III-2’s sister (III-1) and half-brother (III-5) only inherited the maternal mtDNA. Fresh blood sampling and repeated mtDNA sequencing in a second independent laboratory were also performed to rule out the possibility of sample mix-up for III-2 (III-2, column F-G and H-I). Additionally, these samples were further verified using Pacific Bio single molecular sequencing (see Materials and Methods) and by restriction fragment length polymorphism (RFLP) analysis of Family A, and these results were fully consistent with the previous sequencing.

mtdna-inheritance
Biparental mtDNA inheritance pattern shown in Family B. (A) Pedigree of Family B. The black filled symbols indicate the two family members (II-3 and III-2) showing biparental mtDNA transmission. The IDs of five family members tested by whole mtDNA sequencing analysis have been underlined in the pedigree. (B) Schematic of the mtDNA genotype defined by the homoplasmic and/or heteroplasmic variants aligned from the reference mitochondrial genome. Blue bars represent the genotype of paternally derived mtDNA, whereas purple-red and orange-red bars represent maternally derived mtDNA. Entries labeled (D) represent deduced mtDNA genotypes. (C) Summary of the haplogroup and mtDNA variant numbers in Family B.

A Resurgence of the Paternal Transmission Hypothesis

The results presented in this paper make a robust case for paternal transmission of mtDNA. Here, we report biparental mtDNA inheritance (either directly or indirectly) in 17 members in three multigeneration families. Thirteen of these individuals were identified directly by sequencing of the mitochondrial genome, whereas four could be inferred based on preexisting maternal heteroplasmy caused by biparental inheritance in the previous generation.

To further confirm these remarkable results and to exclude the possibility of sample mix-up and/or contamination, the whole mtDNA sequencing procedure was repeated independently in at least two different laboratories by different laboratory technicians with newly obtained blood samples. All results were reproducible, indicating no artifacts or contamination exist. More importantly, the multiple mtDNA variants that were paternally transmitted differ in both number and position among each of these three families as well as the related haplogroup (R0a1 in Family A, K1b2a in Family B, and K2b1a1a in Family C, respectively), providing two distinct forms of evidence supporting transmission of the paternal mtDNA.

Therefore, we have unequivocally demonstrated the existence of biparental mtDNA inheritance as evidenced by the high number and level of mtDNA heteroplasmy in these three unrelated multigeneration families. Most interestingly, the mixed haplogroups in these samples are very reminiscent of the mixed haplogroups found in the 20 studies that were dismissed by Bandelt et al. as due to contamination or sample mix-up. One is forced to wonder how many other instances of individuals with biparental mtDNA inheritance have been dismissed as technical errors, and whether Schwartz and Vissing’s original discovery has really been given the proper follow-up that it deserves. We suspect that these results will initiate a broader reassessment of the topic.

We propose that the paternal mtDNA transmission in these families should be accompanied by segregation of a mutation in one nuclear gene involved in paternal mitochondrial elimination and that there is a high probability that the gene in question operates through one of the pathways identified above.

If I have to be honest, I was stuck with the paternal transmission hypothesis which we were taught in class long ago. I didn’t know it was controversial or dismissed, I just thought it was really exceptional, and I never thought about learning more on the subject.

This paper proves it may be more complicated than that, especially for population genomics purposes, because biparental mtDNA transmission with autosomal dominant-like inheritance puts a serious barrier to a general, simplistic interpretation of mtDNA.

I don’t think it is a blow to all interpretations based on mtDNA, though, because the traditional interpretation should often work statistically. However, one has to be always very careful when saying “if it’s mtDNA from region X, it’s about female exogamy”, especially when samples are from neighbouring regions and similar periods.

The term “uniparental marker” for mtDNA is obviously misleading and shouldn’t be used, and many research papers and interpretations taking mtDNA as strictly uniparental should be taken with a pinch of salt.

Related

Genetic landscape and past admixture of modern Slovenians

slovenes-snp

Open access Genetic Landscape of Slovenians: Past Admixture and Natural Selection Pattern, by Maisano Delser et al. Front. Genet. (2018).

Interesting excerpts (emphasis mine):

Samples

Overall, 96 samples ranging from Slovenian littoral to Lower Styria were genotyped for 713,599 markers using the OmniExpress 24-V1 BeadChips (Figure 1), genetic data were obtained from Esko et al. (2013). After removing related individuals, 92 samples were left. The Slovenian dataset has been subsequently merged with the Human Origin dataset (Lazaridis et al., 2016) for a total of 2163 individuals.

Y chromosome

First, Y chromosome genetic diversity was assessed. A total of 52 Y chromosomes were analyzed for 195 SNPs. The majority of individuals (25, 48.1%) belong to the haplogroup R1a1a1a (R-M417) while the second major haplogroup is represented by R1b (R-M343) including 15 individuals (28.8%). Twelve samples are assigned to haplogroup I (I M170): five and two samples belong to haplogroup I2a (I L460) and I1 (I M253), respectively, while the remaining five samples did not have enough information to be further assigned.

pca-slovenes
PCA of Slovenian samples with European populations (Slovenian_HO_EU dataset). For details regarding the populations included, see Supplementary Table 1.

PCA

Considering the unbalanced sample size of the Slovenian population compared to the other populations included in the dataset, a subset of 20 Slovenian individuals randomly sampled was used.

All Slovenian samples group together with Hungarians, Czechs, and some Croatians (“Central-Eastern European” cluster) as also suggested by the PCA. All Basque individuals with few French and Spanish cluster together (“Basque” cluster) while a “Northern-European” cluster is made of the majority of French, English, Icelanders, Norwegians, and Orcadians. Five populations contributed to the “Eastern-European” cluster including Belarusians, Estonians, Lithuanians, Mordovians, and Russians. Western and South Europe is split into two cluster: the first (“Western European” cluster) includes all Spanish individuals, few French, and some Italians (North Italy) while the second (“Southern-European” cluster) groups Sicilians, Greeks, some Croatians, Romanians, and some Italians (North Italy).

Admixture Pattern and Migration

admixture-slovenians
Modified image, from the paper (Central-East Europeans marked). Unsupervised admixture analysis of Slovenians. Results for K = 5 are showed as it represents the lowest cross-validation error. Slovenian samples show an admixture pattern similar to the neighboring populations such as Croatians and Hungarians. The major ancestral components are: the blue one which is shared with Lithuanians and Russians, followed by the dark green one that is mostly present in Greek samples and the light blue which characterizes Orcadians and English. For population acronyms see Supplementary Table 1.

All Slovenian individuals share common pattern of genetic ancestry, as revealed by ADMIXTURE analysis. The three major ancestry components are the North East and North West European ones (light blue and dark blue, respectively, Figure 3), followed by a South European one (dark green, Figure 3). Contribution from the Sardinians and Basque are present in negligible amount. The admixture pattern of Slovenians mimics the one suggested by the neighboring Eastern European populations, but it is different from the pattern suggested by North Italian populations even though they are geographically close.

Using ALDER, the most significant admixture event was obtained with Russians and Sardinians as source populations and it happened 135 ± 9.31 generations ago (Z-score = 11.54). (…) When tested for multiple admixture events (MALDER), we obtained evidence for one admixture event 165.391 ± 17.1918 generations ago corresponding to ∼2620 BCE (CI: 3101–2139) considering a generation time of 28 years (Figure 4), with Kalmyk and Sardinians as sources.

We then modeled the Slovenian population as target of admixture of ancient individuals from Haak et al. (2015) while computing the f3(Ancient 1, Ancient 2, Slovenian) statistic. The most significant signal was obtained with Yamnaya and HungaryGamba_EN (Z-score = -10.66), followed by MA1 with LBK_EN (Z-score -9.7) and Yamnaya with Stuttgart (Z-score = -8.6) used as possible source populations (Supplementary Figure 5).

We found a significant signal of admixture by using both pairs as ancient sources. Specifically, for the pair Yamnaya and Hungary_EN the admixture event is dated at 134.38 ± 23.69 generations ago (Z-score = 5.26, p-value of 1.5e-07) while for Yamnaya and LBK_EN at 153.65 ± 22.19 generations ago (Z-score = 6.92, p-value 4.4e-12). Outgroup f3 with Yamnaya put Slovenian population close to Hungarians, Czechs, and English, indicating a similar shared drift between these population with the Steppe populations (Supplementary Figure 6).

admixture-events-slovenes
Admixture events identified with ALDER and MALDER. The gray dots represent significant admixture events detected with ALDER using Slovenians as target, the solid line represents the single admixture event detected using MALDER, dashed lines represent the confidence interval. Only the significant results after multiple testing correction are plotted. For ALDER results see Supplementary Table 5.

Not that any of this would come as a surprise, but:

  • R1a-M458 and some R1a-Z280 (xR1a-Z92) lineages (found among Slovenes) were associated with the Slavic expansion, likely with the Prague-Korchak culture, originally stemming probably from peoples of the Lusatian culture. Other R1a-Z280 lineages remained associated with Uralic peoples, and some became Slavicized only recently.
  • PCA keeps supporting the common cluster of certain West, South, and East Slavs in a “Central-Eastern European” cluster, distinct from the “North-Eastern European” cluster formed by modern Finno-Ugrians, as well as ancient Finno-Ugrians of north-eastern Europe who were only recently Slavicized.
  • Admixture supports the same ancient ‘western’ (a core West+South+East Slavic) cluster, and the admixture event with Yamna + Hungary_EN is logically a proxy for Yamna Hungary being at the core of ancestral Central-East population movements related to Bell Beakers in the mid- to late 3rd millennium.

The theory that East Slavs are at the core of the Slavic expansion makes no sense, in terms of archaeology (see Florin Curta’s dismissal of those recent eastern ‘Slavic’ finds, his commentary on 19th century Pan-Slavic crap, or his book on Slavic migrations), in terms of ancient DNA (the earliest Slavs sampled cluster with modern West Slavs, distant from the steppe cluster, unlike Finno-Ugrians), or in terms of modern DNA.

I don’t know where exactly this impulse for the theory of Russia being the cradle of Slavs comes from today (although there are some obvious political trends to revive 19th c. ideas), but it was always clear for everyone, including Russians, that East Slavs had migrated to the east and north and assimilated indigenous Finno-Ugrians, apart from Turkic-, Iranian-, and Caucasian-speaking peoples to the east. Genetics is only confirming what was clear from other disciplines long ago.

Related

The complex origin of Samoyedic-speaking populations

uralic-turkic

Open access Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations, by Karafet et al. Am J Hum Biol (2018) e23194.

Interesting excerpts (emphasis mine):

Siberian groups

Consistent with their origin, Mongolic-speaking Buryats demonstrate genetic similarity with Mongols, and Turkic-speaking Altai-Kizhi and Teleuts are drawn close to CAS groups. The Tungusic-speaking Evenks collected in central and eastern Siberia cluster together and overlap with Yukagirs. Dolgans are widely scattered in the plot, justifying their recent origin from one Evenk clan, Yakuts, and Russian peasants in the 18th century (Popov, 1964). Uralic-speaking populations comprise a very wide cluster with Komi drawn to Europe, and Khants showing a closer affinity with Selkups, Tundra and Forest Nentsi. Yenisey-speaking Kets are intermingled with Selkups. Interestingly, Samoyedic-speaking Nganasans from the Taymyr Peninsula form a separate tight cluster closer to Evenks, Yukagirs, and Koryaks.

pca-siberian-uralic
Principal component analysis (PCA) using the “drop one in” technique for 27 present-day (N = 424) and 6 ancient populations (N = 20). PCA was performed on 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples

ADMIXTURE and the “Siberian component”

Among Siberians, the Komi are primarily Europeans, while Nganasans, Evenks, Yukagirs, and Koryaks are nearly 100% East Asians. At K = 4 finer scale subcontinental structure can be distinguished with the emergence of a “Siberian” component. This component is highly pronounced in the Nganasans. Outside Siberia, this component is present in Germany and in CAS at low frequency. Within ancient cultures, this component has the highest frequency in three BA Karasuk samples. It is also found in Mal’ta, ENE Afanasievo and BA Andronovo, but not in Ust’-Ishim and BA Okunevo. At K = 5, the “Siberian” component is roughly subdivided into two components with different geographic distributions. The “Nganasan” component is frequent in nearly all Siberian populations, except the Komi, Kets and Selkups. The newly derived “Selkup-Ket” component is found at high frequencies in western Siberian populations. It is observed in BA Karasuk and in Mal’ta. At K = 6, the western Siberian “Nentsi-Khant” ancestry component was developed in Forest and Tundra Nentsi, Khants. This component is also present at low levels in EUR, CAS, Tibet, and southern Siberia.

Identity-by-descent

The Dolgans share more segments with the Nganasans than within themselves (54.13 vs 41.72, Mann-Whitney test, P = .000000000001562546). The result is not surprising as the demographic data showed that the Nganasans were subjected to intense assimilation by the Dolgans in the second half of the 20th century (Goltsova, Osipova, Zhadanov, & Villems, 2005). Tundra Nentsi share more IBD with Forest Nentsi than within themselves (83.96 vs 50.3, P = .000055) possibly due to the common origin and long-term gene flow. The Ket and Selkup populations allocate significantly more IBD blocks between populations than with individuals from their own population (121.2 cM vs 85.9 cM for Kets, P = .000008, and 121.2 cM vs 114.9 cM for Selkups, P = .043).

admixture-siberian
ADMIXTURE plot. Clustering of 444 individuals from 27 present-day and 6 ancient populations (281 093 SNPs) assuming K6 to K7 clusters. Individuals are shown as vertical bars colored in ratio to their estimated ancestry within each cluster

Haplogroup N in Siberia

Although Siberia exhibits 42 haplogroups, the vast majority of Siberian Y-chromosomes belong only to 4 of the 18 major clades (N = 46.2%; C = 20.9%; Q = 14.4%; and R = 15.2%). The Y-chromosome haplogroup N is widely spread across Siberia and Eastern Europe (Ilumae et al., 2016; Karafet et al., 2002; Wong et al., 2016) and reaches its maximum frequency among Siberian populations such as Nganasans (94.1%) and Yakuts (91.9%). Within Siberia, two sister subclades N-P43 and N-L708 show different geographic distributions. N-P43 and derived haplogroups N-P63 and N- P362 (phylogenetically identical to N-B478* and N-B170, respectively) (Ilumae et al., 2016) are extremely rare in other major geographic regions. Likely originating in western Siberia, they are limited almost entirely to northwest Siberia, the Volga- Uralic regions, and the Taymyr Peninsula (ie, do not extend to eastern Siberia). Conversely, clade N-L708 is frequent in all Siberian populations except the Kets and Selkups, reaching its highest frequency in the Yakuts (91.9%).

Surprisingly, not a single sign of the proposed reindeer pastoralist horde led by Nganasans into north-eastern Europe. This is strange because “Siberian” migrants hypothetically imposed their language over Indo-Europeans quite recently, apparently after the Iron Age

Interesting comparisons among Siberian groups, though.

Related

Minimal gene flow from western pastoralists in the Bronze Age eastern steppes

jeong-steppes-mongolia

Open access paper Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe, by Jeong et al. PNAS (2018).

Interesting excerpts (emphasis mine):

To understand the population history and context of dairy pastoralism in the eastern Eurasian steppe, we applied genomic and proteomic analyses to individuals buried in Late Bronze Age (LBA) burial mounds associated with the Deer Stone-Khirigsuur Complex (DSKC) in northern Mongolia. To date, DSKC sites contain the clearest and most direct evidence for animal pastoralism in the Eastern steppe before ca. 1200 BCE.

Most LBA Khövsgöls are projected on top of modern Tuvinians or Altaians, who reside in neighboring regions. In comparison with other ancient individuals, they are also close to but slightly displaced from temporally earlier Neolithic and Early Bronze Age (EBA) populations from the Shamanka II cemetry (Shamanka_EN and Shamanka_EBA, respectively) from the Lake Baikal region. However, when Native Americans are added to PC calculation, we observe that LBA Khövsgöls are displaced from modern neighbors toward Native Americans along PC2, occupying a space not overlapping with any contemporary population. Such an upward shift on PC2 is also observed in the ancient Baikal populations from the Neolithic to EBA and in the Bronze Age individuals from the Altai associated with Okunevo and Karasuk cultures.

pca-eurasians-karasuk-khovsgol
Image modified from the article. Karasuk cluster in green, closely related to sample ARS026 in red. Principal Component Analysis (PCA) of selected 2,077 contemporary Eurasians belonging to 149 groups. Contemporary individuals are plotted using three-letter abbreviations for operational group IDs. Group IDs color coded by geographic region. Ancient Khövsgöl individuals and other selected ancient groups are represented on the plot by filled shapes. Ancient individuals are projected onto the PC space using the “lsqproject: YES” option in the smartpca program to minimize the impact of high genotype missing rate.

(…) two individuals fall on the PC space markedly separated from the others: ARS017 is placed close to ancient and modern northeast Asians, such as early Neolithic individuals from the Devil’s Gate archaeological site (22) and present-day Nivhs from the Russian far east, while ARS026 falls midway between the main cluster and western Eurasians.

Upper Paleolithic Siberians from nearby Afontova Gora and Mal’ta archaeological sites (AG3 and MA-1, respectively) (25, 26) have the highest extra affinity with the main cluster compared with other groups, including the eastern outlier ARS017, the early Neolithic Shamanka_EN, and present-day Nganasans and Tuvinians (Z > 6.7 SE for AG3). Main cluster Khövsgöl individuals mostly belong to Siberian mitochondrial (A, B, C, D, and G) and Y (all Q1a but one N1c1a) haplogroups.

mongolia-botai-ehg-ane-cline
The genetic affinity of the Khövsgöl clusters measured by outgroup-f3 and -f4 statistics. (A) The top 20 populations sharing the highest amount of >genetic drift with the Khövsgöl main cluster measured by f3(Mbuti; Khövsgöl, X). (B) The top 15 populations with the most extra affinity with each of the three Khövsgöl clusters in contrast to Tuvinian (for the main cluster) or to the main cluster (for the two outliers), measured by f4(Mbuti, X; Tuvinian/Khövsgöl, Khövsgöl/ARS017/ARS026). Ancient and contemporary groups are marked by squares and circles, respectively. Darker shades represent a larger f4 statistic.

Previous studies show a close genetic relationship between WSH populations and ANE ancestry, as Yamnaya and Afanasievo are modeled as a roughly equal mixture of early Holocene Iranian/ Caucasus ancestry (IRC) and Mesolithic Eastern European hunter-gatherers, the latter of which derive a large fraction of their ancestry from ANE. It is therefore important to pinpoint the source of ANE-related ancestry in the Khövsgöl gene pool: that is, whether it derives from a pre-Bronze Age ANE population (such as the one represented by AG3) or from a Bronze Age WSH population that has both ANE and IRC ancestry.

The amount of WSH contribution remains small (e.g., 6.4 ± 1.0% from Sintashta). Assuming that the early Neolithic populations of the Khövsgöl region resembled those of the nearby Baikal region, we conclude that the Khövsgöl main cluster obtained ∼11% of their ancestry from an ANE source during the Neolithic period and a much smaller contribution of WSH ancestry (4–7%) beginning in the early Bronze Age.

khovsgol-shamanka-sintashta
Admixture modeling of Altai populations and the Khövsgöl main cluster using qpAdm. For the archaeological populations, (A) Shamanka_EBA and (B and C) Khövsgöl, each colored block represents the proportion of ancestry derived from a corresponding ancestry source in the legend. Error bars show 1 SE. (A) Shamanka_EBA is modeled as a mixture of Shamanka_EN and AG3. The Khövsgöl main cluster is modeled as (B) a two-way admixture of Shamanka_EBA+Sintashta and (C) a three-way admixture Shamanka_EN+AG3+Sintashta.

Apparently, then, the first individual with substantial WSH ancestry in the Khövsgöl population (ARS026, of haplogroup R1a-Z2123), directly dated to 1130–900 BC, is consistent with the first appearance of admixed forest-steppe-related populations like Karasuk (ca. 1200-800 BC) in the Altai. Interestingly, haplogroup N1a1a-M178 pops up (with mtDNA U5a2d1) among the earlier Khövsgöl samples.

I will repeat what I wrote recently here: Samoyedic arrived in the Altai with Karasuk and hg R1a-Z645 + Steppe_MLBA-like ancestry, admixed with Altai populations, clustering thus within an Ancient Altai cline. Only later did N1a1a subclades infiltrate Samoyedic (and Ugric) populations, bringing them closer to their modern Palaeo-Siberian cline. The shared mtDNA may support an ancestral EHG-“Siberian” cline, or else a more recent Afanasevo-related origin.

east-uralic-clines
Modified image from Jeong et al. (2018), supplementary materials. The first two PCs summarizing the genetic structure within 2,077 Eurasian individuals. The two PCs generally mirror geography. PC1 separates western and eastern Eurasian populations, with many inner Eurasians in the middle. PC2 separates eastern Eurasians along the north-south cline and also separates Europeans from West Asians. Ancient individuals (color-filled shapes), including two Botai individuals, are projected onto PCs calculated from present-day individuals. Read more.

Also interesting, Q1a2 subclades and ANE ancestry making its appearance everywhere among ancestral Eurasian peoples, as Chetan recently pointed out.

Related

Mongolian tribes cluster with East Asians, closely related to the Japanese

mongolian-sampling

New paper behind paywall Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia, by Bai et al Nature Genetics (2018).

Interesting excerpts (emphasis mine):

Genome sequencing, variant calling, and construction of the Mongolian reference panel. We collected peripheral blood with informed consent from 175 Mongolian individuals representing six distinct tribes/regions in northern China and Mongolia, including the Abaga, Khalkha, Oirat, Buryat, Sonid, and Horchin tribes.

mongolians-pca
Population genetic structure. a, PCA of Mongolian individuals and 1000G samples. Mongolians fill a large, less characterized gap between Admixed/Native Americans and other East Asians in the 1000G project. b, PCA of Mongolians and East Asians of 1000G. The abbreviations of EAS populations were used from reference 11.

The fixation index (FST) was used to estimate pairwise genetic differentiation among our Mongolian samples and 26 modern human populations selected from 1000G (…) the Mongolian tribes cluster with East Asian groups. The Mongolian populations show the smallest differentiation from the CHB, and FST values increase relative to the magnitude of geographical separation. The Buryat are the most differentiated tribe compared with other East Asians (1.82–2.97%), while the Horchin are the least (0.25–1.35%). All tribes are closer to the Japanese (JPT) than the CHS with the exception of the Horchin. Among the tribes, the Abaga, Khalkha, Oirat, and Sonid show the least differentiation from one another (FST < 0.15%)

A PCA places the Mongolians in close genetic proximity to a group of North Asian Siberians, including Altaians, Tuvinians, Evenki, and Yakut, indicating that the Mongolian whole-genome variation panel could be a better proxy for these groups than any populations currently in the 1000G panel

The most common Y-chromosome haplogroups are from the C3 sublineage (41.67%), including C3c (29.17%) and C3b (12.50%), followed by haplogroup O (23.61%), and haplogroup N (18.06%) (…) While haplogroups C and O are primarily restricted to Asia, haplogroup N is present at high frequency in Finns (60.5%), at low frequency in non-Mongolian East Asians (< 1%), and virtually absent throughout the remainder of European and African samples in 1000G

Comparison with Finns

ibd-sharing-mongolian-finns
Distribution of D-values from D-test under the model of [EAS, Mongolians, X, chimpanzee], where X represents the test population and chimpanzee serves as an outgroup. The positive D-value (Z > 3) indicates that the test population (X) is closer to Mongolians than to EAS. The whiskers correspond to range, and the dots to individual data points, box limits are the upper and lower quartiles. The n in each boxplot is 30. All abbreviations of populations in the figure were used from reference 11.

Of the populations included in our study, Mongolians share the second-highest level of IBD with the Finnish people (FIN), behind only Northern Han Chinese (CHB). While Mongolians share more IBD with Europeans (EUR) as a whole compared with other non-EAS people (Fig. 4b), removal of Finns from the Europeans drops the level of sharing to as low as that with South Asians (SAS) or Admixed American (AMR).

There is considerable geographic separation between modern-day Mongolians and Europe. The positive D-statistic that reveal gene flow between Mongolians and Europeans (Fig. 4c), and the high degree of IBD sharing with Finnish people in particular suggest that complex admixture may have occurred throughout northeastern Europe and Siberia. To see whether Mongolians represent the ethnic group in East Asia with the highest level of gene flow with Finnish people, we calculated a D-statistic for each set of populations [Mongolians, X, FIN, Yoruba (YRI)], where X represents a population from Siberia or Northern Canada. Most of the populations reveal an imbalance in allele frequencies that suggests gene flow with Finns (D >0, Z >3), but the greatest imbalance is observed between Siberians/Northern Canadians and Finnish, rather than between Mongolians and Finns. This pattern indicates that northern Asian populations interacted across large geographic ranges.

migration-finns-nganasan
6 migration events, from the supplementary materials.

I guess the 1000G does not have northern Eurasian groups, because the IBD map and values would be lightening up with Palaeo-Siberian peoples

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Corded Ware—Uralic (IV): Hg R1a and N in Finno-Ugric and Samoyedic expansions

haplogroup-uralians

This is the fourth of four posts on the Corded Ware—Uralic identification:

Let me begin this final post on the Corded Ware—Uralic connection with an assertion that should be obvious to everyone involved in ethnolinguistic identification of prehistoric populations but, for one reason or another, is usually forgotten. In the words of David Reich, in Who We Are and How We Got Here (2018):

Human history is full of dead ends, and we should not expect the people who lived in any one place in the past to be the direct ancestors of those who live there today.

Haplogroup N

Another recurrent argument – apart from “Siberian ancestry” – for the location of the Uralic homeland is “haplogroup N”. This is as serious as saying “haplogroup R1” to refer to Indo-European migrations, but let’s explore this possibility anyway:

Ancient haplogroups

We have now a better idea of how many ancient migrations (previously hypothesized to be associated with westward Uralic migrations) look like in genetic terms. From Damgaard et al. (Science 2018):

These serial changes in the Baikal populations are reflected in Y-chromosome lineages (Fig. SA; figs. S24 to S27, and tables S13 and SI4). MAI carries the R haplogroup, whereas the majority of Baikal_EN males belong to N lineages, which were widely distributed across Northern Eurasia (29), and the Baikal_LNBA males all carry Q haplogroups, as do most of the Okunevo_EMBA as well as some present-day Central Asians and Siberians.

The only N1c1 sample comes from Ust’Ida Late Neolithic, 180km to the north of Lake Baikal, which – together with the Bronze Age sample from the Kola peninsula, and the medieval sample from Ust’Ida – gives a good idea of the overall expansion of N subclades and Siberian ancestry among the Circum-Arctic peoples of Eurasia, speakers of Palaeo-Siberian languages.

eurasian-n-subclades
Geographical location of ancient samples belonging to major clade N of the Y-chromosome.

Modern haplogroups

What we should expect from Uralic peoples expanding with haplogroup N – seeing how Yamna expands with R1b-L23, and Corded Ware expands with R1a-Z645 – is to find a common subclade spreading with Uralic populations. Let’s see if it works like that for any N-X subclade, in data from Ilumäe et al. (2016):

haplogroup_n1
Geographic-Distribution Map of hg N3 / N1c / N1a.

Within the Eurasian circum-Arctic spread zone, N3 and N2a reveal a well-structured spread pattern where individual sub-clades show very different distributions:

N1a1-M46 (or N-TAT), formed ca. 13900 BC, TMRCA 9800 BC

   N1a1a2-B187, formed ca. 9800 BC, TMRCA 1050 AD:

The sub-clade N3b-B187 is specific to southern Siberia and Mongolia, whereas N3a-L708 is spread widely in other regions of northern Eurasia.

     N1a1a1a-L708, formed ca. 6800 BC, TMRCA 5400 BC.

       N1a1a1a2-B211/Y9022, formed ca. 5400 BC, TMRCA 1900 BC:

The deepest clade within N3a is N3a1-B211, mostly present in the Volga-Uralic region and western Siberian Khanty and Mansi populations.

         N1a1a1a1a-L392/L1026), formed ca. 4400 BC, TMRCA 2800 BC:

The neighbor clade, N3a3’6-CTS6967, spreads from eastern Siberia to the eastern part of Fennoscandia and the Baltic States

haplogroup_n3a3
Frequency-Distribution Maps of Individual Subclade N3a3 / N1a1a1a1a1a-CTS2929/VL29, probably initially with Akozino warrior-traders.

           N1a1a1a1a1a-CTS2929/VL29, formed ca. 2100 BC, TMRCA 1600 BC:

In Europe, the clade N3a3-VL29 encompasses over a third of the present-day male Estonians, Latvians, and Lithuanians but is also present among Saami, Karelians, and Finns (Table S2 and Figure 3). Among the Slavic-speaking Belarusians, Ukrainians, and Russians, about three-fourths of their hg N3 Y chromosomes belong to hg N3a3.

In the post on Finno-Permic expansions, I depicted what seems to me the most likely way of infiltration of N1c-L392 lineages with Akozino warrior-traders into the western Finno-Ugric populations, with an origin around the Barents sea.

This includes the potential spread of (a minority of) N1c-B211 subclades due to contacts with Anonino on both sides of the Urals, through a northern route of forest and forest-steppe regions (equivalent to the distribution of Cherkaskul compared to Andronovo), given the spread of certain subclades in Ugric populations.

NOTE. An alternative possibility is the association of certain B211 subclades with a southern route of expansion with Pre-Scythian and Scythian populations, under whose influence the Ananino culture emerged -which would imply a very quick infiltration of certain groups of haplogroup N everywhere among Finno-Ugrics on both sides of the Urals – , and also the expansion of some subclades with Turkic-speaking peoples, who apparently expanded with alliances of different peoples. Both (Scythian and Turkic) populations expanded from East Asia, where haplogroup N (including N1c) was present since the Neolithic. I find this a worse model of expansion for upper clades, but – given the YFull estimates and the presence of this haplogroup among Turkic peoples – it is a possibility for many subclades.

           N1a1a1a1a2-Z1936, formed ca. 2800 BC, TMRCA 2400 BC:

The only notable exception from the pattern are Russians from northern regions of European Russia, where, in turn, about two-thirds of the hg N3 Y chromosomes belong to the hg N3a4-Z1936—the second west Eurasian clade. Thus, according to the frequency distribution of this clade, these Northern Russians fit better among other non-Slavic populations from northeastern Europe. N3a4 tends to increase in frequency toward the northeastern European regions but is also somewhat unexpectedly a dominant hg N3 lineage among most Turcic-speaking Volga Tatars and South-Ural Bashkirs.

haplogroup_n3a4
Frequency-Distribution Maps of Individual Subclade N3a4 / N1a1a1a1a2-Z1936, probably with the Samic (first) and Fennic (later) expansions into Paleo-Lakelandic and Palaeo-Laplandic territories.

The expansion of N1a-Z1936 in Fennoscandia is most likely associated with the expansion of Saami into asbestos ware-related territory (like the Lovozero culture) during the Late Iron Age – and mixture with its population – , and with the later Fennic expansion to the east and north, replacing their language.

           N1a1a1a1a4-M2019 (previously N3a2), formed ca. 4400 BC, TMRCA 1700 BC:

Sub-hg N3a2-M2118 is one of the two main bifurcating branches in the nested cladistic structure of N3a2’6-M2110. It is predominantly found in populations inhabiting present-day Yakutia (Republic of Sakha) in central Siberia and at lower frequencies in the Khanty and Mansi populations, which exhibit a distinct Y-STR pattern (Table S7) potentially intrinsic to an additional clade inside the sub-hg N3a2

The second widespread sub-clade of hg N is N2a. (…):

   N1a2b-P43 (B523/FGC10846/Y3184), formed ca. 6800 BC, TMRCA ca. 2700 BC:

The absolute majority of N2a individuals belong to the second sub-clade, N2a1-B523, which diversified about 4.7 kya (95% CI = 4.0–5.5 kya). Its distribution covers the western and southern parts of Siberia, the Taimyr Peninsula, and the Volga-Uralic region with frequencies ranging from from 10% to 30% and does not extend to eastern Siberia (…)

haplogroup_n2
Geographic-Distribution Map of hg N2a1 / N1a2b-P43

The “European” branch suggested earlier from Y-STR patterns turned out to consist of two clades

     N1a2b2a-Y3185/FGC10847, formed ca. 2200 BC, TMRCA 800 BC:

N2a1-L1419, spread mainly in the northern part of that region.

     N1a2b2b1-B528/Y24382, formed ca. 900 BC, TMRCA ca. 900 BC:

N2a1-B528, spread in the southern Volga-Uralic region.

Haplogroup R1a

We also have a good idea of the distribution of haplogroup R1a-Z645 in ancient samples. Its subclades were associated with the Corded Ware expansion, and some of them fit quite well the early expansion of Finno-Permic, Ugric, and Samoyedic peoples to the east.

r1a-z282-z280-z2125-distribution
Modified image, from Underhill et al. (2015). Spatial frequency distributions of Z282 (green) and Z93 (blue) affiliated haplogroups.. Notice the potential Finno-Ugric-associated distribution of Z282 (especially R1a-M558, a Z280 subclade), the expansion of R1a-Z2123 subclades with Central Asian forest-steppe groups.

This is how the modern distribution of R1a among Uralians looks like, from the latest report in Tambets et al. (2018):

  • Among Fennic populations, Estonians and Karelians (ca. 1.1 million) have not suffered the greatest bottleneck of Finns (ca. 6-7 million), and show thus a greater proportion of R1a-Z280 than N1c subclades, which points to the original situation of Fennic peoples before their expansion. To trust Finnish Y-DNA to derive conclusions about the Uralic populations is as useful as relying on the Basque Y-DNA for the language spread by R1b-P312
  • Among Volga-Finnic populations, Mordovians (the closest to the original Uralic cluster, see above) show a majority of R1a lineages (27%).
  • Hungarians (ca. 13-15 million) represent the majority of Ugric (and Finno-Ugric) peoples. They are mainly R1a-Z280, also R1a-Z2123, have little N1c, and lack Siberian ancestry, and represent thus the most likely original situation of Ugric peoples in 4th century AD (read more on Avars and Hungarians).
  • Among Samoyedic peoples, the Selkup, the southernmost ones and latest to expand – that is, those not heavily admixed with Siberian populations – , also have a majority of R1a-Z2123 lineages (see also here for the original Samoyedic haplogroups to the south).

To understand the relevance of Hungarians for Ugric peoples, as well as Estonians, Karelians, and Mordovians (and northern Russians, Finno-Ugric peoples recently Russified) for Finno-Permic peoples, as opposed to the Circum-Arctic and East Siberian populations, one has to put demographics in perspective. Even a modern map can show the relevance of certain territories in the past:

population-density
Population density (people per km2) map of the world in 1994. From Wikipedia.

Summary of ancestry + haplogroups

Fennic and Samic populations seem to be clearly influenced by Palaeo-Laplandic peoples, whereas Volga-Finnic and especially Permic populations may have received gene flow from both, but essentially Palaeo-Siberian influence from the north and east.

The fact that modern Mansis and Khantys offer the highest variation in N1a subclades, and some of the highest “Siberian ancestry” among non-Nganasans, should have raised a red flag long ago. The fact that Hungarians – supposedly stemming from a source population similar to Mansis – do not offer the same amount of N subclades or Siberian ancestry (not even close), and offer instead more R1a, in common with Estonians (among Finno-Samic peoples) and Mordvins (among Volga-Finnic peoples) should have raised a still bigger red flag. The fact that Nganasans – the model for Siberian ancestry – show completely different N1a2b-P43 lineages should have been a huge genetic red line (on top of the anthropological one) to regard them as the Uralian-type population.

We know now that ethnolinguistic groups have usually expanded with massive (usually male-biased) migrations, and that neighbouring locals often ‘resurge’ later without changing the language. That is seen in Europe after the spread of Bell Beakers, with the increase of previous ancestry and lineages in Scandinavia during the formation of the Nordic ethnolinguistic community; in Central-West Europe, with the resurgence of Neolithic ancestry (and lineages) during the Bronze Age over steppe ancestry; and in Central-East Europe (with Unetice or East European Bronze Age groups like Mierzanowice, Trzciniec, or Lusatian) showing an increase in steppe ancestry (and resurge of R1a subclades); none of them represented a radical ethnolinguistic change.

finno-ugric-haplogroup-n
Map of archaeological cultures in north-eastern Europe ca. 8th-3rd centuries BC. [The Mid-Volga Akozino group not depicted] Shaded area represents the Ananino cultural-historical society. Fading purple arrows represent likely stepped movements of subclades of haplogroup N for centuries (e.g. Siberian → Ananino → Akozino → Fennoscandia [N-VL29]; Circum-Arctic → forest-steppe [N1, N2]; etc.). Blue arrows represent eventual expansions of Uralic peoples to the north. Modified image from Vasilyev (2002).

It is not hard to model the stepped arrival, infiltration, and/or resurge of N subclades and “Siberian ancestries”, as well as their gradual expansion in certain regions, associated with certain migrations first – such as the expansions to the Circum-Arctic region, and later the Scythian- and Turkic-related movements – , as well as limited regional developments, like the known bottleneck in Finns, or the clear late expansion of Ugric and Samoyedic languages to the north among nomadic Palaeo-Siberians due to traditions of exogamy and multilingualism. This fits quite well with the different arrival of N (N1c and xN1c) lineages to the different Uralic-speaking groups, and to the stepped appearance of “Siberian ancestry” in the different regions.

The aternative

It is evident that a lot of people were too attached to the idea of Palaeolithic R1b lineages ‘native’ to western Europe speaking Basque languages; of R1a lineages speaking Indo-European and spreading with Yamna; and N lineages ‘native’ to north-eastern Europe and speaking Uralic, and this is causing widespread weeping and gnashing of teeth (instead of the joy of discovering where one’s true patrilineal ancestors come from, and what language they spoke in each given period, which is the supposed objective of genetic genealogy…)

Since an Indo-Germanic branch (as revived now by some in the Copenhaguen group to fit Kristiansen’s theory of the 1980s with recent genetic data) does not make any sense in linguistics, the finding of R1a in Yamna would not have led where some think it would have, because North-West Indo-European would still be the main Late PIE branch in Europe. Don’t take my word for it; take James P. Mallory’s (2013).

mallory-adams-tree
The levels of Indo-European reconstruction, from Mallory & Adams (2006).

If an (unlikely) Indo-Slavonic group were posited, though, such a group would still be bound (with Indo-Iranian) to the steppes with East Yamna/Poltavka (admixing with Abashevo migrants, but retaining its language), developing Sintashta/Potapovka → Srubna/Andronovo, and R1a lineages would have equally undergone the known bottlenecks of the steppes where they replaced R1b-Z2103 – which this eastern group shares with Balkan languages, a haplogroup that links therefore together the Graeco-Aryan group.

As far as I know – and there might be many other similar pet theories out there – there have been proposals of “modern Balto-Slavic-like” populations (in an obvious circular reasoning based on modern populations) in some Scythian clusters of the Iron Age.

NOTE. I will not enter into “Balto-Slavic-like R1a” of the Late Bronze Age or earlier because no one can seriously believe at this point of development of Population Genetics that autosomal similarity predating 1,500+ years the appearance of Slavs equates to their (ethnolinguistic) ancestral population, without a clear intermediate cultural and genetic trail – something we lack today in the Slavic case even for the late Roman period…

finno-saamic-palaeo-germanic-substratum
The Finnic and Saamic separation looks shallower than it actually is. Invisible convergence can be ‘triangulated’ with the help of Germanic layers of mutual loanwords (Häkkinen 2012).

We also know of R1a-Z280 lineages in Srubna, probably expanding to the west. With that in mind, and knowing that Palaeo-Germanic was in close contact with Finno-Samic while both were already separated but still in contact, and that Palaeo-Germanic was also in contact and closely related to a ‘Temematic’ distinct from Balto-Slavic (and also that early Proto-Baltic and Proto-Slavic from the Roman Iron Age and later were in contact with western Uralic) this will be the linguistic map of the Iron Age if R1a is considered to expand Indo-European from some kind of “patron-client” relationship with west Yamna:

palaeo-germanic-italo-celtic
Eastern European language map during the Late Bronze Age / Iron Age, if R1a spread Indo-European languages and Eastern Yamna spoke Indo-Slavonic. Palaeo-Germanic (i.e. Pre- to Proto-Germanic) needs to be in contact with both the Samic Lovozero population and the Fennic west Circum-Arctic one. Italic and Celtic in contact with Pre-Germanic. Germanic in contact with Temematic. Balto-Slavic in contact with Iranian, and near Fennic to allow for later loanwords. For Germanic and Temematic, see Kortlandt (2018).

You might think I have some personal or political reason against this kind of proposals. I haven’t. We have been proposing Indo-European to be the language of the European Union for more than 10 years, so to support R1b-Italo-Celtic in the whole Western Europe, R1a-Germanic in Central and Eastern Europe, and R1a-Indo-Slavonic in the steppes (as the Danish group seems to be doing) has nothing inherently bad (or good) for me. If anything, it gives more reason to support the revival of North-West Indo-European in Europe.

My problem with this proposal is that it is obviously beholden to the notion of the uninterrupted cultural, historic and ethnic continuity in certain territories. This bias is common in historiography (von Falkenhausen 1993), but it extends even more easily into the lesser known prehistory of any territory, and now more than ever some people feel the need to corrupt (pre)history based on their own haplogroups (or the majority haplogroups of their modern countries). However, more than on philosophical grounds, my rejection is based on facts: this picture is not what the combination of linguistic, archaeological, and genetic data shows. Period.

Nevertheless, if Yamna + Corded Ware represented the “big and early expansion” of Germanic and Italo-Celtic peoples proper of the dream Nazi’s Lebensraum and Fascist’s spazio vitale proposals; Uralians were Siberian hunter-gatherers that controlled the whole eastern and northern Russia, and miraculously managed to push (ethnolinguistically) Neolithic agropastoralists to the west during and after the Iron Age, with gradual (and often minimal) genetic impact; and Balto-Slavic peoples were represented by horse riders from Pokrovka/Srubna, hiding then somewhere around the forest-steppe until after the Scythian expansion, and then spreading their language (without much genetic impact) during the early Middle Ages…so be it.

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