The expansion of Indo-Europeans in Y-chromosome haplogroups

yamnaya-corded-ware-y-dna-haplogroups

I have been playing around a little more with GIS tools and haplogroups, and I managed to get some interesting outputs.

I made a video with a timeline of the evolution of Indo-European speakers, according to what is known today about reconstructed languages, prehistoric cultures and ancient DNA:

yamnaya-expansion

NOTE. The video is best viewed in HD 1080p (1920×1080) with a display that allows for this or greater video quality, and a screen big enough to see haplogroup symbols, i.e. tablet or greater. The YouTube link is here. The Facebook link is here.

Based on the results of the past 5 years or so, which have been confirming this combined picture every single time, I doubt there will be much need to change it in any radical way, as only minor details remain to be clarified.

Haplogroup maps

I wanted to publish a GIS tool of my own for everyone to have an updated reference of all data I use for my books.

The most complex GIS tools consume too many resources when used online in a client-server model, so I have to keep that to myself, but there are some ways to publish low quality outputs.

The files below include the possibility to zoom some levels to be able to see more samples, and also to check each one for more information on their ID, attributed culture and label, archaeological site, source paper, subclade (and people responsible for SNP inferences if any), etc.

Some usage notes:

  • Files are large (ca. 20 Mb), so they still take some time to load.
  • For the meaning of symbols and colors (for Y-DNA haplogroups), if there is any doubt, check the video above.
  • Pop-ups with sample information will work on desktop browsers by clicking on them, apparently not on smartphone and related tactile OS. I have changed the settings to show pop-ups on hover, so that it now works (to some extent) on tactile OS.
  • The search tool can look for specific samples according to their official ID, and works by highlighting the symbol of the selected individual (turning it into a bright blue dot), and leading the layer view to the location, but it seems to work best only with some browser and OS settings – in other browsers, you need to zoom out to see where the dot is located. The specific sample with its information could paradoxically disappear in search mode, so you might need to reload and look again for the same site that was highlighted.
  • Latitude and longitude values have been randomly modified to avoid samples overcrowding specific sites, so they are not the original ones.

Y-DNA

There are three versions:

  1. Labels with more specific subclades (including negative SNPs), using YTree for R1b samples (whenever it conflicts with YFull).
  2. Labels with YFull nomenclature.
  3. Simbols without labels (more symbols visible per layer).

y-dna-haplogroups

mtDNA

There are two versions:

  1. Symbols with labels.
  2. Symbols without labels.

NOTE. Because there are too many samples at the starting view, depending on the file you should zoom some levels to start seeing symbols.

mtdna-haplogroups

ADMIXTURE

I have tried running supervised ADMIXTURE models by selecting distant populations based on PCA and qpAdm results, but it seems to work fine only for a small K number, being easily improved when running it unsupervised.

Adding distant populations seems to improve or mess up with the results in unpredictable ways, too, so at this point I doubt ADMIXTURE (or anything other than qpAdm) is actually useful to obtain anything precise in terms of ancestry evolution, although it can give a good overall idea of rough ancestry changes, if K is kept small enough.

Anyway, I will keep trying to find a simple way to show the actual evolution and expansion of “Steppe ancestry”. Since every single run for thousands of samples takes days, I don’t really know if and when I will find something interesting to show…

See also

Vikings, Vikings, Vikings! “eastern” ancestry in the whole Baltic Iron Age

vikings-middle-age

Open access Population genomics of the Viking world, by Margaryan et al. bioRxiv (2019), with a huge new sampling from the Viking Age.

Interesting excerpts (emphasis mine, modified for clarity):

To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago.

Maps illustrating the following texts have been made based on data from this and other papers:

  • Maps showing ancestry include only data from this preprint (which also includes some samples from Sigtuna).
  • Maps showing haplogroup density include Vikings from other publications, such as those from Sigtuna in Krzewinska et al. (2018), and from Iceland in Ebenesersdóttir et al. (2018).
  • Maps showing haplogroups of ancient DNA samples based on their age include data from all published papers, but with slightly modified locations to avoid overcrowding (randomized distance approx. ± 0.1 long. and lat.).

middle-ages-europe-y-dna
Y-DNA haplogroups in Europe during the Viking expansions (full map). See other maps from the Middle Ages.

We find that the transition from the BA to the IA is accompanied by a reduction in Neolithic farmer ancestry, with a corresponding increase in both Steppe-like ancestry and hunter-gatherer ancestry. While most groups show a slight recovery of farmer ancestry during the VA, there is considerable variation in ancestry across Scandinavia. In particular, we observe a wide range of ancestry compositions among individuals from Sweden, with some groups in southern Sweden showing some of the highest farmer ancestry proportions (40% or more in individuals from Malmö, Kärda or Öland).

Ancestry proportions in Norway and Denmark on the other hand appear more uniform. Finally we detect an influx of low levels of “eastern” ancestry starting in the early VA, mostly constrained among groups from eastern and central Sweden as well as some Norwegian groups. Testing of putative source groups for this “eastern” ancestry revealed differing patterns among the Viking Age target groups, with contributions of either East Asian- or Caucasus-related ancestry.

saami-ancestry-vikings
Ancestry proportions of four-way models including additional putative source groups for target groups for which three-way fit was rejected (p ≤ 0.01);

Overall, our findings suggest that the genetic makeup of VA Scandinavia derives from mixtures of three earlier sources: Mesolithic hunter-gatherers, Neolithic farmers, and Bronze Age pastoralists. Intriguingly, our results also indicate ongoing gene flow from the south and east into Iron Age Scandinavia. Thus, these observations are consistent with archaeological claims of wide-ranging demographic turmoil in the aftermath of the Roman Empire with consequences for the Scandinavian populations during the late Iron Age.

Genetic structure within Viking-Age Scandinavia

We find that VA Scandinavians on average cluster into three groups according to their geographic origin, shifted towards their respective present-day counterparts in Denmark, Sweden and Norway. Closer inspection of the distributions for the different groups reveals additional complexity in their genetic structure.

vikings-danish-ancestry
Natural neighbor interpolation of “Danish ancestry” among Vikings.

We find that the ‘Norwegian’ cluster includes Norwegian IA individuals, who are distinct from both Swedish and Danish IA individuals which cluster together with the majority of central and eastern Swedish VA individuals. Many individuals from southwestern Sweden (e.g. Skara) cluster with Danish present-day individuals from the eastern islands (Funen, Zealand), skewing towards the ‘Swedish’ cluster with respect to early and more western Danish VA individuals (Jutland).

Some individuals have strong affinity with Eastern Europeans, particularly those from the island of Gotland in eastern Sweden. The latter likely reflects individuals with Baltic ancestry, as clustering with Baltic BA individuals is evident in the IBS-UMAP analysis and through f4-statistics.

vikings-norwegian-ancestry
Natural neighbor interpolation of “Norwegian ancestry” among Vikings.

For more on this influx of “eastern” ancestry see my previous posts (including Viking samples from Sigtuna) on Genetic and linguistic continuity in the East Baltic, and on the Pre-Proto-Germanic homeland based on hydrotoponymy.

Baltic ancestry in Gotland

Genetic clustering using IBS-UMAP suggested genetic affinities of some Viking Age individuals with Bronze Age individuals from the Baltic. To further test these, we quantified excess allele sharing of Viking Age individuals with Baltic BA compared to early Viking Age individuals from Salme using f4 statistics. We find that many individuals from the island of Gotland share a significant excess of alleles with Baltic BA, consistent with other evidence of this site being a trading post with contacts across the Baltic Sea.

vikings-finnish-ancestry
Natural neighbor interpolation of “Finnish ancestry” among Vikings.

The earliest N1a-VL29 sample available comes from Iron Age Gotland (VK579) ca. AD 200-400 (see Iron Age Y-DNA maps), which also proves its presence in the western Baltic before the Viking expansion. The distribution of N1a-VL29 and R1a-Z280 (compared to R1a in general) among Vikings also supports a likely expansion of both lineages in succeeding waves from the east with Akozino warrior-traders, at the same time as they expanded into the Gulf of Finland.

vikings-y-dna-haplogroup-r1a-z280-over-r1a
Density of haplogroup R1a-Z280 (samples in pink) overlaid over other R1a samples (in green, with R1a-Z284 in cyan) among Vikings.

Vikings in Estonia

(…) only one Viking raiding or diplomatic expedition has left direct archaeological traces, at Salme in Estonia, where 41 Swedish Vikings who died violently were buried in two boats accompanied by high-status weaponry. Importantly, the Salme boat-burial predates the first textually documented raid (in Lindisfarne in 793) by nearly half a century. Comparing the genomes of 34 individuals from the Salme burial using kinship analyses, we find that these elite warriors included four brothers buried side by side and a 3rd degree relative of one of the four brothers. In addition, members of the Salme group had very similar ancestry profiles, in comparison to the profiles of other Viking burials. This suggests that this raid was conducted by genetically homogeneous people of high status, including close kin. Isotope analyses indicate that the crew descended from the Mälaren area in Eastern Sweden thus confirming that the Baltic-Mid-Swedish interaction took place early in the VA.

vikings-swedish-ancestry
Natural neighbor interpolation of “Swedish ancestry” among Vikings.

Viking samples from Estonia show thus ancient Swedes from the Mälaren area, which proves once again that hg. N1a-VL29 (especially subclade N1a-L550) and tiny proportions of so-called “Siberian ancestry” expanded during the Early Iron Age into the whole Baltic Sea area, not only into Estonia, and evidently not spreading with Balto-Finnic languages (since the language influence is in the opposite direction, east-west, Germanic > Finno-Samic, during the Bronze Age).

N1a-VL29 lineages spread again later eastwards with Varangians, from Sweden into north-eastern Europe, most likely including the ancestors of the Rurikid dynasty. Unsurprisingly, the arrival of Vikings with Swedish ancestry into the East Baltic and their dispersal through the forest zone didn’t cause a language shift of Balto-Finnic, Mordvinic, or East Slavic speakers to Old Norse, either…

NOTE. For N1a-Y4339 – N1a-L550 subclade of Swedish origin – as main haplogroup of modern descendants of Rurikid princes, see Volkov & Seslavin (2019) – full text in comments below. Data from ancient samples show varied paternal lineages even among early rulers traditionally linked to Rurik’s line, which explains some of the discrepancies found among modern descendants:

  • A sample from Chernihiv (VK542) potentially belonging to Gleb Svyatoslavich, the 11th century prince of Tmutarakan/Novgorod, belongs to hg. I2a-Y3120 (a subclade of early Slavic I2a-CTS10228) and has 71% “Modern Polish” ancestry (see below).
  • Izyaslav Ingvarevych, the 13th century prince of Dorogobuzh, Principality of Volhynia/Galicia, is probably behind a sample from Lutsk (VK541), and belongs to hg. R1a-L1029 (a subclade of R1a-M458), showing ca. 95% of “Modern Polish” ancestry.
  • Yaroslav Osmomysl, the 12th century Prince of Halych (now in Western Ukraine), was probably of hg. E1b-V13, yet another clearly early Slavic haplogroup.

vikings-y-dna-haplogroup-n1a
Density of haplogroup N1a-VL29, N1a-L550 (samples in pink, most not visible) among Vikings. Samples of hg. R1b in blue, hg. R1a in green, hg. I in orange.

Finnish ancestry

Firstly, modern Finnish individuals are not like ancient Finnish individuals, modern individuals have ancestry of a population not in the reference; most likely Steppe/Russian ancestry, as Chinese are in the reference and do not share this direction. Ancient Swedes and Norwegians are more extreme than modern individuals in PC2 and 4. Ancient UK individuals were more extreme than Modern UK individuals in PC3 and 4. Ancient Danish individuals look rather similar to modern individuals from all over Scandinavia. By using a supervised ancient panel, we have removed recent drift from the signal, which would have affected modern Scandinavians and Finnish populations especially. This is in general a desirable feature but it is important to check that it has not affected inference.

ancient-modern-finns-steppe
PCA of the ancient and modern samples using the ancient palette, showing different PCs. Modern individuals are grey and the K=7 ancient panel surrogate populations are shown in strong colors, whilst the remaining M-K=7 ancient populations are shown in faded colors.

The story for Modern-vs-ancient Finnish ancestry is consistent, with ancient Finns looking much less extreme than the moderns. Conversely, ancient Norwegians look like less-drifted modern Norwegians; the Danish admixture seen through the use of ancient DNA is hard to detect because of the extreme drift within Norway that has occurred since the admixture event. PC4 vs PC5 is the most important plot for the ancient DNA story: Sweden and the UK (along with Poland, Italy and to an extent also Norway) are visibly extremes of a distribution the same “genes-mirror-geography” that was seen in the Ancient-palette analysis. PC1 vs PC2 tells the same story – and stronger, since this is a high variance-explained PC – for the UK, Poland and Italy.

Uniform manifold approximation and projection (UMAP) analysis of the VA and other ancient samples.

Evidence for Pictish Genomes

The four ancient genomes of Orkney individuals with little Scandinavian ancestry may be the first ones of Pictish people published to date. Yet a similar (>80% “UK ancestry) individual was found in Ireland (VK545) and five in Scandinavia, implying that Pictish populations were integrated into Scandinavian culture by the Viking Age.

Our interpretation for the Orkney samples can be summarised as follows. Firstly, they represent “native British” ancestry, rather than an unusual type of Scandinavian ancestry. Secondly, that this “British” ancestry was found in Britain before the Anglo-Saxon migrations. Finally, that in Orkney, these individuals would have descended from Pictish populations.

vikings-british-ancestry
Natural neighbor interpolation of “British ancestry” among Vikings.

(…) ‘UK’ represents a group from which modern British and Irish people all receive an ancestry component. This information together implies that within the sampling frame of our data, they are proxying the ‘Briton’ component in UK ancestry; that is, a pre-Roman genetic component present across the UK. Given they were found in Orkney, this makes it very likely that they were descended from a Pictish population.

Modern genetic variation within the UK sees variation between ‘native Briton’ populations Wales, Scotland, Cornwall and Ireland as large compared to that within the more ‘Anglo-Saxon’ English. This is despite subsequent gene flow into those populations from English-like populations. We have not attempted to disentangle modern genetic drift from historically distinct populations. Roman-era period people in England, Wales, Ireland and Scotland may not have been genetically close to these Orkney individuals, but our results show that they have a shared genetic component as they represent the same direction of variation.

Density of haplogroup R1b-L21 (samples in red), overlaid over all samples of hg. R1b among Vikings (R1b-U106 in green, other R1b-L151 in deep red). To these samples one may add the one from Janakkala in south-western Finland (AD ca. 1300), of hg. R1b-L21, possibly related to these population movements.

For more on Gaelic ancestry and lineages likely representing slaves among early Icelanders, see Ebenesersdóttir et al. (2018).

Y-DNA

As in the case of mitochondrial DNA, the overall distribution profile of the Y chromosomal haplogroups in the Viking Age samples was similar to that of the modern North European populations. The most frequently encountered male lineages were the haplogroups I1, R1b and R1a.

Haplogroup I (I1, I2)

The distribution of I1 in southern Scandinavia, including a sample from Sealand (VK532) ca. AD 100 (see Iron Age Y-DNA maps) proves that it had become integrated into the West Germanic population already before their expansions, something that we already suspected thanks to the sampling of Germanic tribes.

vikings-y-dna-haplogroup-i
Density of haplogroup I (samples in orange) among Vikings. Samples of hg. R1b in blue, hg. R1a in green, N1a in pink.
vikings-y-dna-haplogroup-i1-over-i
Density of haplogroup I1 (samples in red) overlaid over all samples of hg. I among Vikings.

Haplogroup R1b (M269, U106, P312)

Especially interesting is the finding of R1b-L151 widely distributed in the historical Nordic Bronze Age region, which is in line with the estimated TMRCA for R1b-P312 subclades found in Scandinavia, despite the known bottleneck among Germanic peoples under U106. Particularly telling in this regard is the finding of rare haplogroups R1b-DF19, R1b-L238, or R1b-S1194. All of that points to the impact of Bell Beaker-derived peoples during the Dagger period, when Pre-Proto-Germanic expanded into Scandinavia.

Also interesting is the finding of hg. R1b-P297 in Troms, Norway (VK531) ca. 2400 BC. R1b-P297 subclades might have expanded to the north through Finland with post-Swiderian Mesolithic groups (read more about Scandinavian hunter-gatherers), and the ancestry of this sample points to that origin.

However, it is also known that ancestry might change within a few generations of admixture, and that the transformation brought about by Bell Beakers with the Dagger Period probably reached Troms, so this could also be a R1b-M269 subclade. In fact, the few available data from this sample show that it comes from the natural harbour Skarsvågen at the NW end of the island Senja, and that its archaeologist thought it was from the Viking period or slightly earlier, based on the grave form. From Prescott (2017):

In 1995, Prescott and Walderhaug tentatively argued that a dramatic transformation took place in Norway around the Late Neolithic (2350 BCE), and that the swift nature of this transition was tied to the initial Indo-Europeanization of southern and coastal Norway, at least to Trøndelag and perhaps as far north as Troms. (…)

The Bell Beaker/early Late Neolithic, however, represents a source and beginning of these institution and practices, exhibits continuity to the following metal age periods and integrated most of Northern Europe’s Nordic region into a set of interaction fields. This happened around 2400 BCE, at the MNB to LN transition.

NOTE. This particular sample is not included in the maps of Viking haplogroups.

vikings-y-dna-haplogroup-r1b
Density of haplogroup R1b (samples in blue) among Vikings. Samples of hg. I in orange, hg. R1a in green, N1a in pink.
vikings-y-dna-haplogroup-r1b-U106-over-r1b
Density of haplogroup R1b-U106 (samples in green) overlaid over all samples of hg. R1b (other R1b-L23 samples in red) among Vikings.
vikings-y-dna-haplogroup-r1b-P312-over-r1b
Density of R1b-L151 (xR1b-U106) (samples in deep red) overlaid over all samples of hg. R1b (R1b-U106 in green, other R1b-M269 in blue) among Vikings.

Haplogroup R1a (M417, Z284)

The distribution of hg. R1a-M417, in combination with data on West Germanic peoples, shows that it was mostly limited to Scandinavia, similar to the distribution of I1. In fact, taking into account the distribution of R1a-Z284 in particular, it seems even more isolated, which is compatible with the limited impact of Corded Ware in Denmark or the Northern European Plain, and the likely origin of R1a-Z284 in the expansion with Battle Axe from the Gulf of Finland. The distribution of R1a-Z280 (see map above) is particularly telling, with a distribution around the Baltic Sea mostly coincident with that of N1a.

vikings-y-dna-haplogroup-r1a
Density of haplogroup R1a (samples in green) among Vikings. Samples of hg. R1b in blue, of hg. I in orange, N1a in pink.
vikings-y-dna-haplogroup-r1a-z284-over-r1a
Density of haplogroup R1a-Z284 (samples in cyan) overlaid over all samples of hg. R1a (in green, with R1a-Z280 in pink) among Vikings.

Other haplogroups

Among the ancient samples, two individuals were derived haplogroups were identified as E1b1b1-M35.1, which are frequently encountered in modern southern Europe, Middle East and North Africa. Interestingly, the individuals carrying these haplogroups had much less Scandinavian ancestry compared to the most samples inferred from haplotype based analysis. A similar pattern was also observed for less frequent haplogroups in our ancient dataset, such as G (n=3), J (n=3) and T (n=2), indicating a possible non-Scandinavian male genetic component in the Viking Age Northern Europe. Interestingly, individuals carrying these haplogroups were from the later Viking Age (10th century and younger), which might indicate some male gene influx into the Viking population during the Viking period.

vikings-italian-ancestry
Natural neighbor interpolation of “Italian ancestry” among Vikings.

As the paper says, the small sample size of rare haplogroups cannot distinguish if these differences are statistically relevant. Nevertheless, both E1b samples have substantial Modern Polish-like ancestry: one sample from Gotland (VK474), of hg. E1b-L791, has ca. 99% “Polish” ancestry, while the other one from Denmark (VK362), of hg. E1b-V13, has ca. 35% “Polish”, ca. 35% “Italian”, as well as some “Danish” (14%) and minor “British” and “Finnish” ancestry.

Given the E1b-V13 samples of likely Central-East European origin among Lombards, Visigoths, and especially among Early Slavs, and the distribution of “Polish” ancestry among Viking samples, VK362 is probably a close description of the typical ancestry of early Slavs. The peak of Modern Polish-like ancestry around the Upper Pripyat during the (late) Viking Age suggests that Poles (like East Slavs) have probably mixed since the 10th century with more eastern peoples close to north-eastern Europeans, derived from ancient Finno-Ugrians:

vikings-polish-ancestry
Natural neighbor interpolation of “Polish ancestry” among Vikings.

Similarly, the finding of R1a-M458 among Vikings in Funen, Denmark (VK139), in Lutsk, Poland (VK541), and in Kurevanikha, Russia (VK160), apart from the early Slav from Usedom, may attest to the origin of the spread of this haplogroup in the western Baltic after the Bell Beaker expansion, once integrated in both Germanic and Balto-Slavic populations, as well as intermediate Bronze Age peoples that were eventually absorbed by their expansions. This contradicts, again, my simplistic initial assessment of R1a-M458 expansion as linked exclusively (or even mainly) to Balto-Slavs.

antiquity-europe-y-dna
Y-DNA haplogroups in Europe during Antiquity (full map). See other maps of cultures and ancient DNA from Antiquity.

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.

Related

Reproductive success among ancient Icelanders stratified by ancestry

iceland-pca

New paper (behind paywall), Ancient genomes from Iceland reveal the making of a human population, by Ebenesersdóttir et al. Science (2018) 360(6392):1028-1032.

Abstract and relevant excerpts (emphasis mine):

Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.

icelanders
Shared drift of ancient and contemporary Icelanders. (A) Scatterplot of D-statistics reflecting Iceland-specific drift. To aid interpretation, we included values for ancient British-Irish Islanders and a subset of contemporary individuals (who were correspondingly removed from the reference populations).

We estimated the mean Norse ancestry of the settlement population (24 pre-Christians and one early Christian) as 0.566 [95% confidence interval (CI) 0.431–0.702], with a nonsignificant difference betweenmales (0.579) and females (0.521). Applying the same ADMIXTURE analysis to each of the 916 contemporary Icelanders, we obtained a mean Norse ancestry of 0.704 (95% CI 0.699–0.709). Although not statistically significant (t test p = 0.058), this difference is suggestive. A similar difference ofNorse ancestry was observed with a frequency-based weighted least-squares admixture estimator (16), 0.625 [Mean squared error (MSE) = 0.083] versus 0.74 (MSE = 0.0037). Finally, the D-statistic test D(YRI, X; Gaelic, Norse) also revealed a greater affinity between Norse and contemporary Icelanders (0.0004, 95% CI 0.00008–0.00072) than between Norse and ancient Icelanders (−0.0002, 95% CI −0.00056–0.00015). This observation raises the possibility that reproductive success among the earliest Icelanders was stratified by ancestry, as genetic drift alone is unlikely to systematically alter ancestry at thousands of independent loci (fig. S10). We note that many settlers of Gaelic ancestry came to Iceland as slaves, whose survival and freedom to reproduce is likely to have been constrained (17). Some shift in ancestry must also be due to later immigration from Denmark, which maintained colonial control over Iceland from 1380 to 1944 (for example, in 1930 there were 745 Danes out of a total population of 108,629 in Iceland) (18).

icelander-admixture
Shared drift of ancient and contemporary Icelanders. (B) Estimated Norse,
Gaelic, and Icelandic ancestry for ancient Icelanders using ADMIXTURE
in supervised mode.

Five pre-Christian Icelanders (VDP-A5, DAVA9, NNM-A1, SVK-A1 and TGS-A1) fall just outside the space occupied by contemporary Norse in Fig. 3A. That these individuals show a stronger signal of drift shared with contemporary Icelanders is also apparent in the results of ADMIXTURE, run in supervised mode with three contemporary reference populations (Norse, Gaelic, and Icelandic) (Fig. 3B). The correlation between the proportion of Icelandic ancestry from this analysis and PC1 in Fig. 2A is |r| = 0.913.(…)

(…) as the five ancient Icelanders fall well within the cluster of contemporary Scandinavians (Fig. 3C), we conclude that they, or close relatives, likely contributed more to the contemporary Icelandic gene pool than the other pre-Christians. We note that this observation is consistent with the inference that settlers of Norse ancestry had greater reproductive success than those of Gaelic ancestry.

icelanders-y-dna
Haplogroup data, from the paper. Image modified by me, with those close to Gaelic and British/Irish samples (see above Scatterplot of D-statistics and ADMIXTURE data) marked in fluorescent: yellow closer to Gaelic, green less close.

Ancient Icelanders show a clear relation with the typically Norse Y-DNA distribution: I1 / R1a-Z284 / R1b-U106.

  • Among R1a, the picture is uniformly of R1a-Z284 (at least five of the seven reported).
  • There are six samples of I1, with great variation in subclades.
  • Among R1b-L51 subclades (ten samples), there are U106 (at least one sample), L21 (three samples), and another P312 (L238); see above the relationship with those clustering closely with Gaelic samples, marked in fluorescent, which is compatible with Gaelic settlers (predominantly of R1b-L21 lineages) coming to Iceland as slaves.

Probably not much of a surprise, coming from Norse speakers, but they are another relevant reference for comparison with samples of East Germanic tribes, when they appear.

Also, the first reported Klinefelter (XXY) in ancient DNA (sample ID is YGS-B2).

Related:

Ancient DNA samples from Mesolithic Scandinavia show east-west genetic gradient

mesolithic-scandinavia

New pre-print article at BioRxiv, Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation, by Günther et al. (2017), from the Uppsala University (group led by Mattias Jakobsson).

Abstract (emphasis mine):

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans. Finally, we were able to compute a 3D facial reconstruction of a Mesolithic woman from her high-coverage genome, giving a glimpse into an individual’s physical appearance in the Mesolithic.

Interesting is the genetic similarity found with Baltic hunter-gatherers from Zvejnieki:

To investigate the postglacial colonization of Scandinavia, we explored four hypothetical migration routes (primarily based on natural geography) linked to WHGs and EHGs, respectively (Supplementary Information 11); a) a migration of WHGs from the south, b) a migration of EHGs from the east across the Baltic Sea, c) a migration of EHGs from the east and along the north-Atlantic coast, d) a migration of EHGs from the east and south of the Baltic Sea, and combinations of these four migration routes.
(…)
The SHGs from northern and western Scandinavia show a distinct and significantly stronger affinity to the EHGs compared to the central and eastern SHGs (Fig. 1). Conversely, the SHGs from eastern and central Scandinavia were genetically more similar to WHGs compared to the northern and western SHGs (Fig. 1). Using a model-based approach (15, 16), the EHG genetic component of northern and western SHGs was estimated to 55% on average (43-67%) and significantly different (Wilcoxon test, p=0.014) from the average 35% (22-44%) in eastern and south-central SHGs. This average is similar to eastern Baltic hunter-gatherers from Latvia (28) (average 33%, Fig. 1A, Supplementary Information 6). These patterns of genetic affinity within SHGs are in direct contrast to the expectation based on geographic proximity with EHGs and WHGs and do not correlate with age of the sample.
(…)
Combining these isotopic results with the patterns of genetic variation, we suggest an initial colonization from the south, likely by WHGs. A second migration of people who were related to the EHGs – that brought the new pressure blade technique to Scandinavia and that utilized the rich Atlantic coastal marine resources –entered from the northeast moving southwards along the ice-free Atlantic coast where they encountered WHG groups. The admixture between the two colonizing groups created the observed pattern of a substantial EHG component in the northern and the western SHGs, contrary to the higher levels of WHG genetic component in eastern and central SHGs (Fig. 1, Supplementary Information 11).

From the same article, three samples with reported Y-DNA, the three of haplogroup I2 (one more specifically I2a1b). Regarding mtDNA, four samples U5a1 (two of them U5a1d), two samples U4a1, one U4a2.

Featured image: potential migration routes, taken from the supplementary material.

Related: