Palaeolithic Caucasus samples reveal the most important component of West Eurasians

dzudzuana-ancestry-europe

Preprint Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry, by Lazaridis et al. bioRxiv (2018).

Interesting excerpts:

We analyzed teeth from two individuals 63 recovered from Dzudzuana Cave, Southern Caucasus, from an archaeological layer previously dated to ~27-24kya (…). Both individuals had mitochondrial DNA sequences (U6 and N) that are consistent with deriving from lineages that are rare in the Caucasus or Europe today. The two individuals were genetically similar to each other, consistent with belonging to the same population and we thus analyze them jointly.

(…) our results prove that the European affinity of Neolithic Anatolians does not necessarily reflect any admixture into the Near East from Europe, as an Anatolian Neolithic-like population already existed in parts of the Near East by ~26kya. Furthermore, Dzudzuana shares more alleles with Villabruna-cluster groups than with other ESHG (Extended Data Fig. 5b), suggesting that this European affinity was specifically related to the Villabruna cluster, and indicating that the Villabruna affinity of PGNE populations from Anatolia and the Levant is not the result of a migration into the Near East from Europe. Rather, ancestry deeply related to the Villabruna cluster was present not only in Gravettian and Magdalenian-era Europeans but also in the populations of the Caucasus, by ~26kya. Neolithic Anatolians, while forming a clade with Dzudzuana with respect to ESHG, share more alleles with all other PGNE (Extended Data Fig. 5d), suggesting that PGNE share at least partially common descent to the exclusion of the much older samples from Dzudzuana.

dzudzuana-anatolia-pca
Ancient West Eurasian population structure. PCA of key ancient West Eurasians, including additional populations (shown with grey shells), in the space of outgroup f4-statistics (Methods).

Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirms that the Taforalt population was mixed, but instead of specifying gene flow from the ancestors of Natufians into the ancestors of Taforalt as originally reported, we infer gene flow in the reverse direction (into Natufians). The Neolithic population from Morocco, closely related to Taforalt is also consistent with being descended from the source of this gene flow, and appears to have no admixture from the Levantine Neolithic (Supplementary Information 166 section 3). If our model is correct, Epipaleolithic Natufians trace part of their ancestry to North Africa, consistent with morphological and archaeological studies that indicate a spread of morphological features and artifacts from North Africa into the Near East. Such a scenario would also explain the presence of Y-chromosome haplogroup E in the Natufians 170 and Levantine farmers, a common link between the Levant and Africa.

(…) we cannot reject the hypothesis that Dzudzuana and the much later Neolithic Anatolians form a clade with respect to ESHG (P=0.286), consistent with the latter being a population largely descended from Dzudzuana-like pre-Neolithic populations whose geographical extent spanned both Anatolia and the Caucasus. Dzudzuana itself can be modeled as a 2-way mixture of Villabruna-related ancestry and a Basal Eurasian lineage.

In qpAdm modeling, a deeply divergent hunter-gatherer lineage that contributed in relatively unmixed form to the much later hunter-gatherers of the Villabruna cluster is specified as contributing to earlier hunter-gatherer groups (Gravettian Vestonice16: 35.7±11.3% and Magdalenian ElMiron: 60.6±11.3%) and to populations of the Caucasus (Dzudzuana: 199 72.5±3.7%, virtually identical to that inferred using ADMIXTUREGRAPH). In Europe, descendants of this lineage admixed with pre-existing hunter-gatherers related to Sunghir3 from Russia for the Gravettians and GoyetQ116-1 from Belgium for the Magdalenians, while in the Near East it did so with Basal Eurasians. Later Europeans prior to the arrival of agriculture were the product of re-settlement of this lineage after ~15kya in mainland Europe, while in eastern Europe they admixed with Siberian hunter-gatherers forming the WHG-ANE cline of ancestry [See PCA above]. In the Near East, the Dzudzuana-related population admixed with North African-related ancestry in the Levant and with Siberian hunter-gatherer and eastern non-African-related ancestry in Iran and the Caucasus. Thus, the highly differentiated populations at the dawn of the Neolithic were primarily descended from Villabruna Cluster and Dzudzuana-related ancestors, with varying degrees of additional input related to both North Africa and Ancient North/East Eurasia whose proximate sources may be clarified by future sampling of geographically and temporally intermediate populations.

qpgraph-dzudzuana
An admixture graph model of Paleolithic West Eurasians. An automatically generated admixture graph models fits populations (worst Z-score of the difference between estimated and fitted f-statistics is 2.7) or populations (also including South_Africa_HG, worst Z-score is 3.5). This is a simplified model assuming binary admixture events and is not a unique solution (Supplementary Information section 2). Sampled populations are shown with ovals and select labeled internal nodes with rectangles.

Interesting excerpts from the supplementary materials:

From our analysis of Supplementary Information section 3, we showed that these sources are indeed complex, and only one of these (WHG, represented by Villabruna) appears to be a contributor to all the remaining sources. This should not be understood as showing that hunter-gatherers from mainland Europe migrated to the rest of West Eurasia, but rather that the fairly homogeneous post-15kya population of mainland Europe labeled WHG appear to represent a deep strain of ancestry that seems to have contributed to West Eurasians from the Gravettian era down to the Neolithic period.

Villabruna is representative of the WHG group. We also include ElMiron, the best sample from the Magdalenian era as we noticed that within the WHG group there were individuals that could not be modeled as a simple clade with Villabruna but also had some ElMiron-related ancestry. Ddudzuana is representative of the Ice Age Caucasus population, differentiated from Villabruna by Basal Eurasian ancestry. AG3 represents ANE/Upper Paleolithic Siberian ancestry, sampled from the vicinity of Lake Baikal, while Russia_Baikal_EN related to eastern Eurasians and represents a later layer of ancestry from the same region of Siberia as AG3 Finally, Mbuti are a deeply diverged African population that is used here to represent deep strains of ancestry (including Basal Eurasian) prior to the differentiation between West Eurasians and eastern non-Africans that are otherwise not accounted for by the remaining five sources. Collectively, we refer to this as ‘Basal’ or ‘Deep’ ancestry, which should be understood as referring potentially to both Basal Eurasian and African ancestry.

It has been suggested that there is an Anatolia Neolithic-related affinity in hunter-gatherers from the Iron Gates. Our analysis confirms this by showing that this population has Dzudzuana-related ancestry as do many hunter-gatherer populations from southeastern Europe, eastern Europe and Scandinavia. These populations cannot be modeled as a simple mixture of Villabruna and AG3 but require extra Dzudzuana-related ancestry even in the conservative estimates, with a positive admixture proportion inferred for several more in the speculative ones. Thus, the distinction between European hunter-gatherers and Near Eastern populations may have been gradual in pre-Neolithic times; samples from the Aegean (intermediate between those from the Balkans and Anatolia) may reveal how gradual the transition between Dzudzuana-like Neolithic Anatolians and mostly Villabruna-like hunter-gatherers was in southeastern Europe.

ancient-modern-european-admixture
Modified image (cut, with important samples marked). Modeling present-day and ancient West-Eurasians. Mixture proportions computed with qpAdm (Supplementary Information section 4). The proportion of ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the 365 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and other (e.g., Sub-Saharan African) ancestry. (a) ‘Conservative’ estimates. Each population 367 cannot be modeled with fewer admixture events than shown.

Villabruna: This type of ancestry differentiates between present-day Europeans and non-Europeans within West Eurasia, attaining a maximum of ~20% in the Baltic in accordance with previous observations and with the finding of a later persistence of significant hunter-gatherer ancestry in the region. Its proportion drops to ~0% throughout the Near East. Interestingly, a hint of such ancestry is also inferred in all North African populations west of Libya in the speculative proportions, consistent with an archaeogenetic inference of gene flow from Iberia to North Africa during the Late Neolithic.

ElMiron: This type of ancestry is absent in present-day West Eurasians. This may be because most of the Villabruna-related ancestry in Europeans traces to WHG populations that lacked it (since ElMiron-related ancestry is quite variable within European hunter-gatherers). However, ElMiron ancestry makes up only a minority component of all WHG populations sampled to date and WHG-related ancestry is a minority component of present-day Europeans. Thus, our failure to detect it in present day people may be simply be too little of it to detect with our methods.

Dzudzuana: Our analysis identifies Dzudzuana-related ancestry as the most important component of West Eurasians and the one that is found across West Eurasian-North African populations at ~46-88% levels. Thus, Dzudzuana-related ancestry can be viewed as the common core of the ancestry of West Eurasian-North African populations. Its distribution reaches its minima in northern Europe and appears to be complementary to that of Villabruna, being most strongly represented in North Africa, the Near East (including the Caucasus) and Mediterranean Europe. Our results here are expected from those of Supplementary Information section 3 in which we modeled ancient Near Eastern/North African populations (the principal ancestors of present-day people from the same regions) as deriving much of their ancestry from a Dzudzuana-related source. Migrations from the Near East/Caucasus associated with the spread of the Neolithic, but also the formation of steppe population introduced most of the Dzudzuana-related ancestry present in Europe, although (as we have seen above) some such ancestry was already present in some pre-agricultural hunter-gatherers in Europe.

AG3: Ancestry related to the AG3 sample from Siberia has a northern distribution, being strongly represented in both central-northern Europe and the north Caucasus.

Russia_Baikal_EN: Ancestry related to hunter-gatherers from Lake Baikal in Siberia (postdating AG3) appears to have affected primarily northeastern European populations which have been previously identified as having East Eurasian ancestry; some such ancestry is also identified for a Turkish population from Balıkesir, likely reflecting the Central Asian ancestry of Turkic speakers which has been recently confirmed directly in an Ottoman sample from Anatolia.

So, here we have the explanation for the “bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East” inferred from Anatolian hunter-gatherers.

Related

Expansion of haplogroup G2a in Anatolia possibly associated with the Mature Aceramic period

anatolian-hunter-gatherer-sampling

Preprint Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, by Feldman et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

Anatolian hunter-gatherers experienced climatic changes during the last glaciation and inhabited a region that connects Europe to the Near East. However, interactions between Anatolia and Southeastern Europe in the later Upper Palaeolithic/Epipalaeolithic are so far not well documented archaeologically. Interestingly, a previous genomic study showed that present-day Near-Easterners share more alleles with European hunter-gatherers younger than 14,000 BP (‘Later European HG’) than with earlier ones (‘Earlier European HG’). With ancient genomic data available, we could directly compare the Near-Eastern hunter-gatherers (AHG and Natufian) with the European ones. As is the case for present-day Near-Easterners, the Near-Eastern hunter-gatherers share more alleles with the Later European HG than with the Earlier European HG, shown by the significantly positive statistic D(Later European HG, Earlier European HG; AHG/Natufian, Mbuti). Among the Later European HG, recently reported Mesolithic hunter-gatherers from the Balkan peninsula, which geographically connects Anatolia and central Europe (‘Iron Gates HG’), are genetically closer to AHG when compared to all the other European hunter-gatherers, as shown in the significantly positive statistic D(Iron_Gates_HG, European hunter-gatherers; AHG, Mbuti/Altai). Iron Gates HG are followed by Epigravettian and Mesolithic individuals from Italy and France (Villabruna and Ranchot respectively) as the next two European hunter-gatherers genetically closest to AHG. Iron Gates HG have been suggested to be genetically intermediate between WHG and eastern European hunter-gatherers (EHG) with an additional unknown ancestral component.

anatolian-hunter-gatherer-pca
Ancient genomes (marked with color-filled symbols) projected onto the principal components 5 computed from present-day west Eurasians (grey circles) (fig. S4). The geographic location of each ancient group is marked in (A). Ancient individuals newly reported in this study are additionally marked with a black dot inside the symbol

We find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively). The affinity detected by the above D-statistic can be explained by gene flow from Near-Eastern hunter-gatherers into the ancestors of Iron Gates or by a gene flow from a population ancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of both. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestry 5 component (α), which is prevalent in the Near East but undetectable in European hunter-gatherers. Following a published approach, we estimated α to be 24.8 ± 5.5 % in AHG and 38.5 ± 5.0 % in Natufians, consistent with previous estimates for the latter. Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). However, Iron Gates can be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 %, suggesting that unidirectional gene flow from the Near East to Europe alone is insufficient to explain the extra affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East. Presumably, this Southeastern European ancestral population later spread into central Europe during the post-last-glacial maximum (LGM) period, resulting in the observed late Pleistocene genetic affinity between the Near East and Europe.

near-eastern-european-hg
Basal Eurasian ancestry proportions (α) as a marker for Near-Eastern gene flow. Mixture proportions inferred by qpAdm for AHG and the Iron Gates HG are schematically represented. The lower schematic shows the expected α in Iron Gates HG under 10 assumption of unidirectional gene flow, inferred from α in the AHG source population. The observed α for Iron Gates HG is considerably smaller than expected thus, the unidirectional gene flow from the Near East to Europe is not sufficient to explain the above affinity.

While ancestry is not always relevant to distinguish certain population movements (see here), especially – as in this case – when there are few samples (thus neither geographically nor chronologically representative) and no previous model to test, it seems that ancestry and Y-DNA show a great degree of continuity in Anatolia since the Palaeolithic until the Neolithic, at least in the sampled regions. C1a2 appears in Europe since ca. 40,000 years ago (viz. Kostenki, Goyet, Vestonice, etc., and later emerges again in the Balkans after the Anatolian Neolithic expansion, probably a resurge of European groups).

The potential transition of a G2a-dominated agricultural society – that is later prevalent in Anatolian and European farmers – may have therefore happened during the Aceramic III period (ca. 8000 BC), a process of haplogroup expansion probably continuing through the early part of the Pottery Neolithic, as the society based on kinship appeared (Rosenberg and Erim-Özdoğan 2011). There is still much to know about the spread of ceramic technology and southwestern Asia domesticate complex, though.

anatolian-palaeolithic-hg

Without a proper geographical sampling, representative of previous and posterior populations, it is impossible to say. But the expansion of R1b-L754 through Anatolia to form part of the Villabruna cluster (and also the Iron Gates HG) seems perfectly possible with this data, although this paper does not help clarify the when or how. We have seen significant changes in ancestry happen within centuries with expanding populations admixing with locals. Palaeolithic sampling – like this one – shows few individuals scattered geographically over thousands of km and chronologically over thousands of years…

Related

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

jena-isba8

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):

finland-medieval-admixture

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:

mongol-bronze-age-pca

mongol-bronze-age-f4-ancestry

Mitogenomes suggest rapid expansion of domesticated horse before 3500 BC

Open access Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives, by Yoon et al. PLOS One (2018).

Abstract (emphasis mine)

The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski’s horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breeds across the globe using a Bayesian coalescent approach as well as Bayesian inference and maximum likelihood methods. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Thoroughbred horse breed was not directly related to the Przewalski’s horse which has been regarded as the closest taxon to the all domestic horses and the only true wild horse species left in the world. Our phylogenomic analyses also supported that there was no apparent correlation between geographic origin or breed and the evolution of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100–111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My). Bayesian skyline plot revealed that the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500–11,000 years ago, which coincide with the start of domestication. This is the first phylogenomic study on the Thoroughbred racehorse in association with its spatio-temporal dynamics. The database and genetic history information of Thoroughbred mitogenomes obtained from the present study provide useful information for future horse improvement projects, as well as for the study of horse genomics, conservation, and in association with its geographical distribution.

horse-domestication
Bayesian skyline plot (BSP) based on mitochondrial genome sequences from 167 modern horses.
The dark line in the BSP represents the estimated effective population size through time. The green area represents the 95% highest posterior density confidence intervals for this estimate.

Interesting excerpts:

We carried out a Bayesian coalescent approach using extended mitochondrial genome sequences from 167 horses in order to further assess the timescale of horse domestication. Here, we first calculated the time of the most recent common ancestor of Thoroughbred horses. Our analysis revealed the age of the most recent common ancestor of the racing horse to be around 8,100–111,500 years old. This estimate is much younger than that of the most recent common ancestor of the global horses, which has been estimated at 0.7286 Mys old.

phylogenetic-tree-horses
Bayesian maximum clade credibility phylogenomic tree on the ground of the mitochondrial genome sequences of 167 modern horses.
The data set (16,432 base pairs) was also analyzed phylogenetically using Bayesian inference (BI) and maximum likelihood (ML) methods which showed the same topologies. 95% Highest Posterior Density of node heights are shown by blue bars. Groups are marked by a “G”. Numbers at the nodes represent (left to right): posterior probabilities (≥0.80) for the BI tree and bootstrap values (≥70%) for the ML tree. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Results of phylogenomic analyses also uncovered no apparent association between geographic origin or breed and heterogeneity of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100–111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My).

On the domestication time of modern horses, there have been several publications derived from both archaeological [49–51] and molecular [11–12, 23, 48] evidences. D’Andrade [49] reported that the origin of domestic horses was around 4,000 years ago. Ludwig et al. [50] stated the domestication time to be about 5,000 years ago, while Anthony [51] noted that horse rearing by humans may have occurred approximately 6,000 years ago. Subsequently, on the basis of mitochondrial genome sequences, Lippold et al. [11] and Achilli et al. [12] postulated domestication time to be about 6,000–8,000 and 6,000–7,000 years ago, respectively. Warmuth [48] dated domestication time to 5,500 years ago based on autosomal genotype data, while Orlando et al. [23] claimed that Przewalski’s and domestic horse populations diverged 38,000–72,000 years ago based on analysis of genome sequences. In contrast to the previous hypothesized date of horse domestication, the results of our Bayesian skyline plot (BSP) analysis depict a rapid expansion of the horse population approximately 5,500–11,000 years ago, which coincides with the start of domestication.

It seems that we will not have an update on horse aDNA from the ISBA 8, so we will have to make do with this for the moment.

Related

Modern Sardinians show elevated Neolithic farmer ancestry shared with Basques

sardinia-europe-relation

New paper (behind paywall), Genomic history of the Sardinian population, by Chiang et al. Nature Genetics (2018), previously published as a preprint at bioRxiv (2016).

#EDIT (18 Sep 2018): Link to read paper for free shared by the main author.

Interesting excerpts (emphasis mine):

Our analysis of divergence times suggests the population lineage ancestral to modern-day Sardinia was effectively isolated from the mainland European populations ~140–250 generations ago, corresponding to ~4,300–7,000 years ago assuming a generation time of 30 years and a mutation rate of 1.25 × 10−8 per basepair per generation. (…) in terms of relative values, the divergence time between Northern and Southern Europeans is much more recent than either is to Sardinia, signaling the relative isolation of Sardinia from mainland Europe.

We documented fine-scale variation in the ancient population ancestry proportions across the island. The most remote and interior areas of Sardinia—the Gennargentu massif covering the central and eastern regions, including the present-day province of Ogliastra— are thought to have been the least exposed to contact with outside populations. We found that pre-Neolithic hunter-gatherer and Neolithic farmer ancestries are enriched in this region of isolation. Under the premise that Ogliastra has been more buffered from recent immigration to the island, one interpretation of the result is that the early populations of Sardinia were an admixture of the two ancestries, rather than the pre-Neolithic ancestry arriving via later migrations from the mainland. Such admixture could have occurred principally on the island or on the mainland before the hypothesized Neolithic era influx to the island. Under the alternative premise that Ogliastra is simply a highly isolated region that has differentiated within Sardinia due to genetic drift, the result would be interpreted as genetic drift leading to a structured pattern of pre-Neolithic ancestry across the island, in an overall background of high Neolithic ancestry.

sardinia-pca
PCA results of merged Sardinian whole-genome sequences and the HGDP Sardinians. See below for a map of the corresponding regions.

We found Sardinians show a signal of shared ancestry with the Basque in terms of the outgroup f3 shared-drift statistics. This is consistent with long-held arguments of a connection between the two populations, including claims of Basque-like, non-Indo-European words among Sardinian placenames. More recently, the Basque have been shown to be enriched for Neolithic farmer ancestry and Indo-European languages have been associated with steppe population expansions in the post-Neolithic Bronze Age. These results support a model in which Sardinians and the Basque may both retain a legacy of pre-Indo-European Neolithic ancestry. To be cautious, while it seems unlikely, we cannot exclude that the genetic similarity between the Basque and Sardinians is due to an unsampled pre-Neolithic population that has affinities with the Neolithic representatives analyzed here.

density-nuraghi-sardinia-genetics
Left: Geographical map of Sardinia. The provincial boundaries are given as black lines. The provinces are abbreviated as Cag (Cagliari), Cmp (Campidano), Car (Carbonia), Ori (Oristano), Sas (Sassari), Olb (Olbia-tempio), Nuo (Nuoro), and Ogl (Ogliastra). For sampled villages within Ogliastra, the names and abbreviations are indicated in the colored boxes. The color corresponds to the color used in the PCA plot (Fig. 2a). The Gennargentu region referred to in the main text is the mountainous area shown in brown that is centered in western Ogliastra and southeastern Nuoro.
Right: Density of Nuraghi in Sardinia, from Wikipedia.

While we can confirm that Sardinians principally have Neolithic ancestry on the autosomes, the high frequency of two Y-chromosome haplogroups (I2a1a1 at ~39% and R1b1a2 at ~18%) that are not typically affiliated with Neolithic ancestry is one challenge to this model. Whether these haplogroups rose in frequency due to extensive genetic drift and/or reflect sex-biased demographic processes has been an open question. Our analysis of X chromosome versus autosome diversity suggests a smaller effective size for males, which can arise due to multiple processes, including polygyny, patrilineal inheritance rules, or transmission of reproductive success. We also find that the genetic ancestry enriched in Sardinia is more prevalent on the X chromosome than the autosome, suggesting that male lineages may more rapidly trace back to the mainland. Considering that the R1b1a2 haplogroup may be associated with post-Neolithic steppe ancestry expansions in Europe, and the recent timeframe when the R1b1a2 lineages expanded in Sardinia, the patterns raise the possibility of recent male-biased steppe ancestry migration to Sardinia, as has been reported among mainland Europeans at large (though see Lazaridis and Reich and Goldberg et al.). Such a recent influx is difficult to square with the overall divergence of Sardinian populations observed here.

sardinian-admixture
Mixture proportions of the three-component ancestries among Sardinian populations. Using a method first presented in Haak et al. (Nature 522, 207–211, 2015), we computed unbiased estimates of mixture proportions without a parameterized model of relationships between the test populations and the outgroup populations based on f4 statistics. The three-component ancestries were represented by early Neolithic individuals from the LBK culture (LBK_EN), pre-Neolithic huntergatherers (Loschbour), and Bronze Age steppe pastoralists (Yamnaya). See Supplementary Table 5 for standard error estimates computed using a block jackknife.

Once again, haplogroup R1b1a2 (M269), and only R1b1a2, related to male-biased, steppe-related Indo-European migrations…just sayin’.

Interestingly, haplogroup I2a1a1 is actually found among northern Iberians during the Neolithic and Chalcolithic, and is therefore associated with Neolithic ancestry in Iberia, too, and consequently – unless there is a big surprise hidden somewhere – with the ancestry found today among Basques.

NOTE. In fact, the increase in Neolithic ancestry found in south-west Ireland with expanding Bell Beakers (likely Proto-Beakers), coupled with the finding of I2a subclades in Megalithic cultures of western Europe, would support this replacement after the Cardial and Epi-Cardial expansions, which were initially associated with G2a lineages.

I am not convinced about a survival of Palaeo-Sardo after the Bell Beaker expansion, though, since there is no clear-cut cultural divide (and posterior continuity) of pre-Beaker archaeological cultures after the arrival of Bell Beakers in the island that could be identified with the survival of Neolithic languages.

We may have to wait for ancient DNA to show a potential expansion of Neolithic ancestry from the west, maybe associated with the emergence of the Nuragic civilization (potentially linked with contemporaneous Megalithic cultures in Corsica and in the Balearic Islands, and thus with an Iberian rather than a Basque stock), although this is quite speculative at this moment in linguistic, archaeological, and genetic terms.

Nevertheless, it seems that the association of a Basque-Iberian language with the Neolithic expansion from Anatolia (see Villar’s latest book on the subject) is somehow strengthened by this paper. However, it is unclear when, how, and where expanding G2a subclades were replaced by native I2 lineages.

Related

A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP

indo-european-indo-iranian-migrations

New open access paper (in Chinese) A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP, by liu et al. Acta Anthropologica Sinitica (2018)

Abstract:

The Keriyan, Lopnur and Dolan peoples are isolated populations with sparse numbers living in the western border desert of our country. By sequencing and typing the complete Y-chromosome of 179 individuals in these three isolated populations, all mutations and SNPs in the Y-chromosome and their corresponding haplotypes were obtained. Types and frequencies of each haplotype were analyzed to investigate genetic diversity and genetic structure in the three isolated populations. The results showed that 12 haplogroups were detected in the Keriyan with high frequencies of the J2a1b1 (25.64%), R1a1a1b2a (20.51%), R2a (17.95%) and R1a1a1b2a2 (15.38%) groups. Sixteen haplogroups were noted in the Lopnur with the following frequencies: J2a1 (43.75%), J2a2 (14.06%), R2 (9.38%) and L1c (7.81%). Forty haplogroups were found in the Dolan, noting the following frequencies: R1b1a1a1 (9.21%), R1a1a1b2a1a (7.89%), R1a1a1b2a2b (6.58%) and C3c1 (6.58%). These data show that these three isolated populations have a closer genetic relationship with the Uygur, Mongolian and Sala peoples. In particular, there are no significant differences in haplotype and frequency between the three isolated populations and Uygur (f=0.833, p=0.367). In addition, the genetic haplotypes and frequencies in the three isolated populations showed marked Eurasian mixing illustrating typical characteristics of Central Asian populations.

population-distribution-map
Figure 1. The populations distribution map. Left: Uluru. Center: Dali Yabuyi. Right: Kaerqu.

My knowledge of written Chinese is almost zero, so here are some excerpts with the help of Google Translate:

The source of 179 blood samples used in the study is shown in Figure 1. The Keriyan blood samples were collected from Dali Yabuyi Township, Yutian County (39 samples). The blood samples of the Lopnur people were collected from Kaerqu Township, Yuli County (64 cases); the blood samples of the Dolan people were collected from the town of Uluru, Awati County (76).

haplotype-frequency-uighur
Columns one and two are the Keriyan haplotypes and frequencies, respectively; the third and fourth columns are the Lopnur haplotypes and frequencies; the last four columns are the Daolang haplotypes and frequencies.

The composition and frequency of the Keriyan people’s haplogroup are closest to those of the Uighurs, and both Principal Component Analysis and Phylogenetic Tree Analysis show that their kinship is recent. We initially infer that the Keriyan are local desert indigenous people. They have a connection with the source of the Uighurs. Chen et al. [42] studied the patriarchal and maternal genetic analysis of the Keriyan people and found that they are not descendants of the Tibetan ethnic group in the West. The Keriyan people are a mixed group of Eastern and Western Europeans, which may originate from the local Vil group. Duan Ranhui [43] and other studies have shown that the nucleotide variability and average nucleotide differences in the Keriyan population are between the reported Eastern and Western populations. The phylogenetic tree also shows that the populations in Central Asia are between the continental lineage of the eastern population and the European lineage of the western population, and the genetic distance between the Keriyan and the Uighurs is the closest, indicating that they have a close relationship.

y-chromosome-pca

Regarding the origin of the Lopnur people, Purzhevski judged that it was a mixture of Mongolians and Aryans according to the physical characteristics of the Lopnur people. In 1934, the Sino-Swiss delegation discovered the famous burials of the ancient tombs in the Peacock River. After research, they were the indigenous people before the Loulan period; the researcher Yang Lan, a researcher at the Institute of Cultural Relics of the Chinese Academy of Social Sciences, said that the Lopnur people were descendants of the ancient “Landan survivors”. However, the Loulan people speaking an Indo-European language, and the Lopnur people speaking Uyghur languages contradict this; the historical materials of the Western Regions, “The Geography of the Western Regions” and “The Western Regions of the Ming Dynasty” record the Uighurs who lived in Cao Cao in the late 17th and early 18th centuries. Because of the occupation of the land by the Junggar nobles and their oppression, they fled. Some of them were forced to move to the Lop Nur area. There are many similar archaeological discoveries and historical records. We have no way to determine their accuracy, but they are at different times, and there is a great difference in what is heard in the same region. (…) The genetic characteristics of modern Lopnur people are the result of the long-term ethnic integration of Uyghurs, Mongols, and Europeans. This is also consistent with the similarity of the genetic structure of the Y chromosome of Lopnur in this study with the Uighurs and Mongolians. For example, the frequency of J haplogroup is as high as 59.37%, while J and its downstream sub-haplogroup are mainly distributed in western Europe, West Asia and Central Asia; the frequency of O, R haplogroup is close to that of Mongolians.

y-chromosome-frequency
1) KA: Keriya, LB: Rob, DL: Daolang, HTW: Hetian Uygur, HTWZ: and Uygur, TLFW: Turpan Uighur, HZ: Hui, HSKZ: Kazakh, WZBKZ: Wuhuan Others, TJKZ: Tajik, KEKZZ: Kirgiz, TTEZ: Tatar, ELSZ: Russian XBZ: Xibo, MGZ: Mongolian, SLZ: Salar, XJH: Xinjiang Han, GSH: Gansu Han, GDH: Guangdong Han SCH: Sichuan Han. 2) Reference population data source literature 19-22. After the population names in the table have been marked, all the shorthands in the text are referred to in this table. 3) Because the degree of haplotypes of each reference population is different to each sub-group branch, the sub-group branches under the same haplogroup are merged when the population haplogroup data is aggregated, for example: for haplogroup G Some people are divided into G1a and G2a levels, others are assigned to G1, G2, and G3, while some people can only determine G this time. Therefore, each subgroup is merged into a single group G.

According to Ming History·Western Biography, the Mongolians originated from the Mobei Plateau and later ruled Asia and Eastern Europe. Mongolia was established, and large areas of southern Xinjiang and Central Asia were included. Later, due to the Mongolian king’s struggle for power, it fell into a long-term conflict. People of the land fled to avoid the war, and the uninhabited plain of the lower reaches of the Yarkant River naturally became a good place to live. People from all over the world gathered together and called themselves “Dura” and changed to “Dang Lang”. The long-term local Uyghur exchanges that entered the southern Mongolian monks and “Dura” were gradually assimilated [44]. According to the report, locals wore Mongolian clothes, especially women who still maintained a Mongolian face [45]. In 1976, the robes and waistbands found in the ancient time of the Daolang people in Awati County were very similar to those of the ancients. Dalang Muqam is an important part of Daolang culture. It is also a part of the Uyghur Twelve Muqam, and it retains the ancient Western culture, but it also contains a larger Mongolian culture and relics. The above historical records show that the Daolang people should appear in the Chagatai Khanate and be formed by the integration of Mongolian and Uighur ethnic groups. Through our research, we also found that the paternal haplotype of the Daolang people is contained in both Uygur and Mongolian, and the main haplogroups are the same, whereas the frequencies are different (see Table 3). The principal component analysis and the NJ analysis are also the same. It is very close to the Uyghur and the Mongolian people, which establishes new evidence for the “mixed theory” in molecular genetics.

main-haplogroup-uighur
Genetic relationship between the three isolated populations: the Uygur and the Mongolian is the closest, and the main haplogroup can more intuitively compare the source composition of the genetic structure of each population. Haplogroups C, D, and O are mainly distributed in Asia as the East Asian characteristic haplogroup; haplogroups G, J, and R are mainly distributed in continental Europe, and the high frequency distribution is in Europe and Central Asia.

If the nomenclature follows a recent ISOGG standard, it appears that:

The presence of exclusively R1a-Z93 subclades and the lack of R1b-M269 samples is compatible with the expansion of R1a-Z93 into the area with Proto-Tocharians, at the turn of the 3rd-2nd millennium BC, as suggested by the Xiaohe samples, supposedly R1a(xZ93).

Now that it is obvious from ancient DNA (as it was clear from linguistics) that Pre-Tocharians separated earlier than other Late PIE peoples, with the expansion of late Khvalynsk/Repin into the Altai, at the end of the 4th millennium, these prevalent R1a (probably Z93) samples may be showing a replacement of Pre-Tocharian Y-DNA with the Andronovo expansion already by 2000 BC.

Lacking proper assessment of ancient DNA from Proto-Tocharians, this potential early Y-DNA replacement is still speculative*. However, if that is the case, I wonder what the Copenhagen group will say when supporting this, but rejecting at the same time the more obvious Y-DNA replacement in East Yamna / Poltavka in the mid-3rd millennium with incoming Corded Ware-related peoples. I guess the invention of an Indo-Tocharian group may be near…

*NOTE. The presence of R1b-M269 among Proto-Tocharians, as well as the presence of R1b-M269 among Tarim Basin peoples in modern and ancient times is not yet fully discarded. The prevalence of R1a-Z93 may also be the sign of a more recent replacement by Iranian peoples, before the Mongolian and Turkic expansions that probably brought R1b(xM269).

Also, the presence of R1b (xM269) samples in east Asia strengthens the hypothesis of a back-migration of R1b-P297 subclades, from Northern Europe to the east, into the Lake Baikal area, during the Early Mesolithic, as found in the Botai samples and later also in Turkic populations – which are the most likely source of these subclades (and probably also of Q1a2 and N1c) in the region.

Related

Long-term matrilineal continuity in a nonisolated region of Tuscany

iron_age_europe_mediterranean

New paper (behind paywall) The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany, by Leonardi et al. Am J Phys Anthr (2018).

EDIT (10 SEP 2018): The main author has shared an open access link to read the PDF.

Interesting excerpts:

Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.

We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups.

In all cases, a simple model of a long-term genealogical continuity proved to fit the data better, and sometimes much better, than the alternative hypothesis of discontinuity.

The low number of samples analyzed requires some caution in the interpretation. Because we did not test for gene flow, it is at this stage impossible to reject it, but our results suggest at least significant levels of genealogical continuity. Moreover, as it has not been possible to obtain more precise information on the age of the Eneolithic samples, they were grouped together considering the average archaeological period of interest, which may cause a bias in the analyses. (…)

tuscany
Geographic location of the samples considered in this work

(…) clearly, our samples show high levels of continuity when considering the whole Tuscan region as a genetic reservoir during the Iron Age.

The posterior distributions of the parameters confirm a high degree of genetic isolation in the sampled population, with very small values for the female effective population sizes across time. Such values, in particular the Neolithic ones, are in accord with the estimates obtained in similar studies, both in Tuscany (Ghirotto et al., 2013) and in France (Rivollat et al., 2017).

tuscany-genetic-diversity

Taken at their face value, our results do not show any major shift in the composition of the maternal ancestry of the population, across 50 centuries. This does not mean that no demographic process of relevance has affected the population, and indeed the higher diversity accumulating in time is the likely consequence of immigrating people, enriching the mitochondrial gene pool.

(…) the population of the current Lucca province appears to have retained very ancient mitochondrial features, despite occupying a geographical corridor between the Ligurian and the Tyrrhenian coast, and despite not showing the persistence of unique cultural traits through the centuries.

tuscany-genetic-diversity-hap

Another possibility is that that the different populations passing through the area (Etruscans, Romans, and Lombards) had a consistent social and/or sex bias. An example of similar patterns has been observed several times. Between the Late Neolithic and the Early Bronze Age, female exogamy in patrilocal society has been observed in Southern Germany (Knipper et al., 2017); during the Bronze Age the migrations toward Europe from the steppes appears to have consisted prevalently of males (Goldberg, Günther, Rosenberg, & Jakobsson, 2017); and in more recent periods in the Canary Islands, the female ancestry maintains a significant amount of autochthonous lineages, while the male ancestry was strongly influenced by the European colonization (Fregel et al., 2009, b).

It is well known that military invasions may not have a significant genetic impact upon the invaded population (Schiffels et al., 2016; Sokal, Oden, Walker, Di Giovanni, & Thomson, 1996;Weale,Weiss, Jager, Bradman, & Thomas, 2002), especially at the mitochondrial level, because of the limited size of a sustainable army, and of the fact that armies are generally composed mostly or only of males. Even if a substantial share of invaders decided to remain and settle the region, this form of gene flow would affect mostly or only the paternal lineages, rather than the maternal ones. We can also hypothesize the immigration of a number of people (e.g., Romans, Lombards) that may have acted as ruler of the region, remaining socially (and so genetically) separated by the local population, and leaving few (if any) traces in the gene pools of the local population.

tuscany-mtdna-haplogroups
Supporting Information, Table S1 New ancient samples genotyped

We expect to see that certain migrations since the Iron Age – like the Celtic and Roman ones – were somehow different from previous ones, where, at least since the Neolithic, male-dominated expansions were the rule.

If, however, male-biased expansions are also seen during the Iron Age – probably driven by particular subclades then – , this would certainly justify the continuity of admixture in certain regions in spite of these population expansions, and thus the importance of Y-DNA to track more recent language changes.

One of the most interesting details of the upcoming paper of Italic peoples will be the Y-DNA (and admixture) of Etruscans compared to other neighbouring peoples, given the known conflicting theories regarding their recent vs. older origin in the East before the historical record.

Related

Early Medieval Alemannic graveyard shows diverse cultural and genetic makeup

alemannic-niederstotzingen

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:

Introduction

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. (…)

alemannic-haplogroup

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

alemannic-pca
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.

Kinship

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).

alemannic-family
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.

Conclusion

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.

Related

Viking Age town shows higher genetic diversity than Neolithic and Bronze Age

sigtuna-vikings

Open access Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town, by Krzewińska et al., Current Biology (2018).

Interesting excerpts (emphasis mine, some references deleted for clarity):

The town of Sigtuna in eastern central Sweden was one of the pioneer urban hubs in the vast and complex communicative network of the Viking world. The town that is thought to have been royally founded was planned and organized as a formal administrative center and was an important focal point for the establishment of Christianity [19]. The material culture in Sigtuna indicates that the town had intense international contacts and hosted several cemeteries with a Christian character. Some of them may have been used by kin-based groups or by people sharing the same sociocultural background. In order to explore the character and magnitude of mobility and migration in a late Viking Age town, we generated and analyzed genomic (n = 23) and strontium isotope (n = 31) data from individuals excavated in Sigtuna.

y-dna-vikings

The mitochondrial genomes were sequenced at 1.5× to 367× coverage. Most of the individuals were assigned to haplogroups commonly found in current-day Europeans, such as H, J, and U [14, 26, 27]. All of these haplotypes are present in Scandinavia today.

The Y chromosome haplogroups were assigned in seven males. The Y haplogroups include I1a, I2a, N1a, G2a, and R1b. Two identified lineages (I2a and N1a) have not been found in modern-day Sweden or Norway [28, 29]. Haplogroups I and N are associated with eastern and central Europe, as well as Finno-Ugric groups [30]. Interestingly, I2a was previously identified in a middle Neolithic Swedish hunter-gatherer dating to ca. 3,000 years BCE [31].

In Sigtuna, the genetic diversity in the late Viking Age was greater than the genetic diversity in late Neolithic and Bronze Age cultures (Unetice and Yamnaya as examples) and modern East Asians; it was on par with Roman soldiers in England but lower than in modern-day European groups (GBR and FIN; Figure 2B). Within the town, the group excavated at church 1 has somewhat greater diversity than that at cemetery 1. Interestingly, the diversity at church 1 is nearly as high as that observed in Roman soldiers in England, which is remarkable, since the latter was considered to be an exceptionally heterogeneous group in contemporary Europe [39].

pca-vikings
A PCA plot visualising all 23 individuals from Sigtuna used in ancient DNA analyses (m – males, f – females).

Different sex-related mobility patterns for Sigtuna inhabitants have been suggested based on material culture, especially ceramics. Building on design and clay analyses, some female potters in Sigtuna are thought to have grown up in Novgorod in Rus’ [40]. Moreover, historical sources mention female mobility in connection to marriage, especially among the elite from Rus’ and West Slavonic regions [41, 42]. Male mobility is also known from historical sources, often in connection to clergymen moving to the town [43].

Interestingly, we found a number of individuals from Sigtuna to be genetically similar to the modern-day human variation of eastern Europeans, and most harbor close genetic affinities to Lithuanians (Figure 2A). The strontium isotope ratios in 28 adult individuals with assigned biological sex and strontium values obtained from teeth (23 M1 and five M2) show that 70% of the females and 44% of the males from Sigtuna were non-locals (STAR Methods). The difference in migrant ratios between females and male mobility patterns was not statistically significant (Fisher’s exact test, p = 0.254 for 28 individuals and p = 0.376 for 16 individuals). Hence, no evidence of a sex-specific mobility pattern was found.

(…) As these social groups are not mirrored by our genetic or strontium data, this suggests that the inclusion in them was not based on kinship. Therefore, it appears as if socio-cultural factors, not biological bonds, governed where people were interred (i.e., the choice of cemetery).

diversity-yamna
Average pairwise genetic diversity measured in complete Sigtuna, St. Gertrud (church 1) and cemetery 1 (the Nunnan block) compared to both ancient and modern populations ranked by time period (Yamnaya, Unetice, and GBR-Roman, Roman Age individuals from Great Britain; GBR-AS, Anglo-Saxon individuals from Great Britain; GBR-IA, Iron Age individuals from Great Britain; JPT-Modern, presentday Japanese from Tokyo; FIN-Modern, present-day Finnish; GBR-Modern, present-day British; GIHModern, present-day Gujarati Indian from Houston, Texas). Error bars show ±2 SEs.

Interesting from this paper is the higher genetic (especially Y-DNA) diversity found in more recent periods (see e.g. here) compared to Neolithic and Bronze Age cultures, which is probably the reason behind some obviously wrong interpretations, e.g. regarding links between Yamna and Corded Ware populations.

The sample 84001, a “first-generation short-distance migrant” of haplogroup N1c-L392 (N1a in the new nomenclature) brings yet more proof of how:

  • Admixture changes completely within a certain number of generations. In this case, the N1c-L392 sample clusters within the genetic variation of modern Norwegians, near to the Skane Iron Age sample, and not with its eastern origin (likely many generations before).
  • This haplogroup appeared quite late in Fennoscandia but still managed to integrate and expand into different ethnolinguistic groups; in this case, this individual was probably a Viking of Nordic language, given its genetic admixture and its non-local (but neighbouring Scandinavian) strontium values.

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The father tongue and mother tongue hypotheses in Indo-European populations

New paper (behind paywall) Reconciling the father tongue and mother tongue hypotheses in Indo-European populations, by Zhang et al. National Science Review (2018) nwy083.

Interesting excerpts:

Here, we reassessed the correlation between genetic and linguistic characteristics in 34 modern IE populations (Fig. 1a), for which all four types of datasets (lexicon, phonemes, Y-chromosomal composition, and mitochondrial DNA (mtDNA) composition) are available. We assembled compositions of the Y-chromosomal and mtDNA haplogroups or paragroups from the corresponding IE populations, which reflect paternal and maternal lines, respectively (…)

Neighbour-Nets were constructed to delineate the differences between 34 IE population groups clustering at the genetic and linguistic levels (Fig. 2). The reticulations within each net reflect conflicting signals against tree-like structures and support incompatible groupings [21]. These structures are likely produced by potential horizontal transmissions between populations or languages such as admixture, and potential parallel evolution in linguistics as well [22]. The Neighbour-Net for Y-chromosomes with substantial reticulations shows complicated relationships among IE populations (Fig. 2a), indicating a substantial historical population contact and admixture among the males. In contrast, the Neighbour-Net for mtDNA in Fig. 2b clearly illustrates an East-West geographic polarization, indicating two major IE populations in matrilineages: Indo-Iranian and European. (…)

y-dna-mtdna-phoneme-lexicon
Neighbour-Nets of 34 Indo-European populations calculated from the Euclidean distance matrices using (a) Y-chromosomal haplogroups and (b) mtDNA haplogroups; Neighbour-Nets of IE languages calculated from the Hamming distance matrices using (c) lexicon and (d) phonemes. The colours in the legend correspond to the language groups.

The language learning by local women could constitute the reason for unbalanced correlation of mtDNA to lexicon and phonemes. Due to the social prestige of male immigrants, their local spouses have to adopt the language of their husbands and pass it to future generations [6, 10, 15]. This process is second language acquisition and easily develops language fossilization [31]. The language fossilization is a linguistic mechanism that a learner of a second language tends to preserve some linguistic features of the first language, and develops a form of inter-language [31]. Under this circumstance, women can easily replace the lexicon from another [21], but attempt to retain local accents influenced by their native language [32]. In other words, women change to adopt the same word usage as their husbands in daily life but still speak using their own pronunciation. In mixed-language marriages with these male immigrants, women prefer to pass down their inter-languages to offspring [10, 33]. As a result, it yields the correlation between mtDNA and phonemes we observed. Hence, we courageously proposed a hypothetical scenario in Indo-European populations that lexical system of language dominated by their father, while the phonemic system of language determined by their mother.

I am not a fan of this kind of statistical studies for Comparative Grammar, and there are many pitfalls just by looking at this paper superficially: use of modern languages and modern haplogroup distributions, improper classification of phonemes – as is usual in glottochronological studies – , etc… Which render their results ipso facto unacceptable.

But just yesterday I was discussing where the Copenhagen group and their fans were going to end up when Yamna samples turn out not to be the origin of haplogroup R1a-Z645 expansion, and Anthony’s proposal of a patron-client relationship came up. Since the Danish workgroup is always one step behind, such a reactionary view seems like a reasonable assumption for the future.

This mother tongue vs. father tongue theory is another good possibility for what we are going to see, then, when they use e.g. the exogamy of eastern Corded Ware groups with Yamna to explain the adoption of the language. Maybe that’s what Kristiansen’s invented Yamna → Corded Ware arrows mean… Anything to prove that Corded Ware peoples were Indo-European speakers.

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