Showing posts with label Sweden. Show all posts
Showing posts with label Sweden. Show all posts

April 24, 2014

More ancient Scandinavians (Skoglund, Malmström et al. 2014)

A new paper has just appeared in Science which adds new ancient Swedish hunter-gatherer samples, as well as a new Gökhem2 Swedish farmer. Much lower quality data from the same archaeological sites were studied in 2012 by much the same team, but the new study has sequenced several new Pitted Ware individuals from Ajvide, as well as a  Mesolithic Swede.

The Swedish hunter-gatherers appear to be similar to those of Lazaridis et al. (2013) in that their ancestry is a mixture of both European hunter-gatherers like LaBrana1 and ~15% of something related to MA1, which seems quite close to the 19% of ANE ancestry for the older Motala hunter-gatherer also from Sweden. The finding of Y-haplogroup I2a1 also parallels the Motala hunter-gatherers, so everything seems quite consistent with the Mesolithic Swedes being genetically very close to the Pitted Ware Neolithic ones. However, there is one difference in that the new hunter-gatherers were ancestral for SLC24A5 while the Motala one was derived (this is the "skin lightening" allele that was curiously missing in both Iberia and Luxembourg hunter-gatherers).

The authors also find that the Iceman and Gökhem2 are a mixture of Basal Eurasians and something related to hunter-gatherers. A interesting new detail is that the Swedish farmer had more of the hunter-gatherer ancestry than the Iceman (the estimated difference in their non-Basal Eurasian ancestry is 77.2-56=21.2%) which seems reasonably close to the 16% difference in the related "Atlantic_Baltic" ancestry for the previous lower-quality Gok4 farmer and the Iceman I estimated in 2012.

Finally, the authors also study the genetic diversity of the Swedish hunter-gatherers:
The Scandinavian Neolithic hunter-gatherer group had significantly lower conditional nucleotide diversity (0.181±0.0015) compared to the Scandinavian Neolithic farmer group (0.201±0.0038, Figs 3A and S9). While the specific properties of ancient DNA may still affect comparisons with sequence data from modern-day individuals, the conditional nucleotide diversity in the hunter-gatherers was also lower than in any modern-day European and a Chinese population (22) analyzed using the same approach as for the ancient groups.
It is not easy to estimate nucleotide diversity with low coverage data (because you can't tell whether a sample is heterozygous in some position if you only have a handful of reads covering it), but the authors cleverly use the fact that they have multiple individuals from the hunter-gatherer population to estimate this. The low diversity in hunter-gatherers also parallels the finding of low genetic diversity in the Luxembourgeois Mesolithic hunter-gatherer, so it does seem that hunter-gatherers in Europe were a very low diversity population, which seems reasonable for people engaging in foraging (which does not allow for growth to large population numbers) and having ancestors who endured the Ice Age in Europe.

The last few months have been extremely generous in new ancient DNA studies and I hope that more stuff is coming this year as in 2013.

UPDATE: Also important (from the Independent):
“We see clear evidence that people from hunter-gatherer groups were incorporated into farming groups as they expanded across Europe. This might be clues towards something that happens also when agriculture spread to other parts of the world,” Dr Skoglund said.

Science DOI: 10.1126/science.1253448

Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers

Pontus Skoglund, Helena Malmström et al.

Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains contentious. Population-genomic data from eleven Scandinavian Stone-Age human remains suggest that hunter-gatherers had lower genetic diversity than farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone-Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone-Age foraging groups were historically in low numbers, likely due to oscillating living conditions or restricted carrying-capacity, and that they were partially incorporated into expanding farming groups.

Link

October 07, 2013

Migration from Sweden to Poland during the Early Bronze Age

Proof of human migration from Sweden to Poland during the Early Bronze Age
During the Early Bronze Age there was a very high level of territorial mobility of the Únětice culture in Silesia, a large community inhabiting the south western territories of Poland approximately 4 000 years ago. This is found in a new doctoral thesis from the University of Gothenburg which also conclusively confirms the first case of human long-distance overseas journey to Silesia from Scandinavia, probably from southern Sweden.

'Over 3800 years ago, a young male, possibly born in Skåne, made a journey of over 900 kilometers south, to Wroclaw in Poland. He died violently in Wroclaw, killed by Úněticean farmers, possibly due to romance with two local females, who were murdered together with him. This 'Bronze Age love story', with no happy end today is the first case of Swedish-Polish contacts in history ever', concludes archaeologist Dalia Pokutta, author of the thesis.
Here is the thesis, titled:  Population Dynamics, Diet and Migrations of the Únětice Culture in Poland.

September 27, 2013

Reconstructing the Human Past using Ancient and Modern Genomes

A reader alerts me to the availability of this comprehensive summary (pdf) which references a number of new manuscripts. A quite interesting picture which extends the author's previous work on ancient DNA from Sweden. Note the addition of a "a Mesolithic individual from Stora Förvar cave on the Stora Karlsö Island in the Baltic Sea" and more Ajv Neolithic hunters and Go:k Neolithic TRB farmers compared to the Science paper.



Reconstructing the Human Past using Ancient and Modern Genomes

PONTUS SKOGLUND

Abstract

Skoglund, P. 2013. Reconstructing the Human Past using Ancient and Modern Genomes. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1069. 68 pp. Uppsala. ISBN 978-91-554-8744-7. The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modernday contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.

Link (pdf)

September 19, 2013

Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe (preprint)

This is an abstract of a preprint not currently available, and seems to build on previous work by the same authors.

Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe

Pontus Skoglund et al.

Recent ancient DNA studies have provided new evidence for prehistoric population structure associated with the contentious transition to an agricultural lifestyle in Europe. In this study, we infer human population structure and history in Holocene Europe by generating ancient genomic sequence data from 9 Scandinavian individuals associated with the foraging Pitted Ware Culture and the agricultural Funnel Beaker Culture (TRB). We obtained up to 1.1x coverage of the genomes for the nine individuals allowing direct comparisons of the two groups. We show that the Neolithic Scandinavian individuals show remarkable population structure corresponding to their cultural association. Looking beyond Scandinavia, we integrate this data with ancient genomes from Southern Europe and find that the Tyrolean Iceman from an agricultural context is most similar to Scandinavian individuals from a farming context, whereas Mesolithic Iberian hunter-gatherers are most similar to Scandinavian hunter-gatherers, opposite to what would have been predicted from their geographical origins. This finding shows that among these individuals, lifestyle is the major determinant of genetic ancestry rather than geography. Comparisons with modern populations reveal a latitudinal relationship where Southern European populations such as Sardinians are closely related with the genetic variation of the agricultural groups, whereas hunter-gatherer individuals appear to have the closest relationship with Baltic populations such as Lithuanians and present-day Scandinavians. Our results also demonstrate that while Middle Eastern populations are not the most similar to Neolithic farmers, this observation can be explained by African-related admixture in more recent times for Middle Eastern groups, which, once accounted for, reveals that the other major component of their ancestry resembles Neolithic farmers. While present-day Scandinavian populations are intermediate between the two groups, consistent with admixture, they appear genetically slightly closer to Neolithic hunter-gatherers than Neolithic farmers. This suggests a model where initial colonization by agricultural populations was followed by later admixture with hunter-gatherer populations or gene flow from other regions.

Link

May 10, 2013

Links between Mycenaeans and Scandinavia

Three papers on a similar theme. An excerpt from a source mentioned in the second paper:
Det visar sig att alla undersökta svenska föremål utom ett enda - en slaggbit - kommer från gruvor och malmfyndigheter från platser på Cypern, Sardinien, Iberiska halvön, Massif Central i nuvarande Frankrike, Tyrolen samt Brittiska öarna. Kopparn har transporterats hit och i utbyte har man skeppat tillbaka stora mängder bärnsten. Fram träder en bild av en tid då internationella kontakter över stora vatten var självklarheter, och det redan cirka 2000 år innan vikingarna gav sig iväg på sina färder. [Google Translate]: It turns out that all examined Swedish subject except one - a slaggbit - comes from mines and ore deposits from sites in Cyprus, Sardinia, the Iberian Peninsula, the Massif Central in the current France, Tyrol and the British Isles. Copper has been transported, and in return it has been shipped back large amounts of amber. What emerges is a picture of a time when international contacts over large water was obvious, and there are already some 2000 years before the Vikings set off on their journeys.
From the third paper:
Both the lead isotope and chemical analyses have undoubtedly showed that the copper from the 33 Scandinavian Bronze Age artefacts diverges significantly from Scandinavian copper ores and that the copper must have been imported from elsewhere. The results furthermore indicate that there are variations in metal supply that are related to chronology, in resemblance with artefacts from Scandinavia as well as from other parts of Europe indicating analogous trade routes for copper, during the respective periods. Maritime networks and changing sources of metal seem to have been a key feature for Scandinavia in the Bronze Age.
Archaeology, Ethnology and Anthropology of Eurasia

Volume 40, Issue 2, June 2012, Pages 99–103

Grave Circle B at Mycenae in the Context of Links Between the Eastern Mediterranean and Scandinavia in the Bronze Age

I.B. Gubanov

Artifacts from royal burial graves Gamma and Omicron of grave circle B at Mycenae attest to cultural ties between the Eastern Mediterranean elite and that of the Scandinavian Early Bronze Age (mid- and late 2nd millennium BC). The appearance of the running spiral motif and representations of ships with rams in Scandinavia coincide with the beginning of the Mycenaean civilization. These facts, along with the finds of Baltic amber only in the royal burials at Mycenae but not in Crete, suggest that a principal role in the introduction of these cultural elements in Scandinavia during the Scandinavian Bronze Age (periods I–III according to Montelius) was played by the Mycenaean elite.

Link

Journal of Geography and Geology Vol 5, No 1 (2013)

The Bronze Age in SE Sweden Evidence of Long-Distance Travel and Advanced Sun Cult 

Nils-Axel Mörner, Bob G. Lind

The Bronze Age of Scandinavia (1750-500 BC) is characterized by the sudden appearance of bronze objects in Scandinavia, the sudden mass appearance of amber in Mycenaean graves, and the beginning of bedrock carvings of huge ships. We take this to indicate that people from the east Mediterranean arrived to Sweden on big ships over the Atlantic, carrying bronze objects from the south, which they traded for amber occurring in SE Sweden in the Ravlunda-Vitemölla–Kivik area. Those visitors left strong cultural imprints as recorded by pictures and objects found in SE Sweden. This seems to indicate that the visits had grown to the establishment of a trading centre. The Bronze Age of Österlen (the SE part of Sweden) is also characterized by a strong Sun cult recorded by stone monuments built to record the annual motions of the Sun, and rock carvings that exhibit strict alignments to the annual motions of the Sun. Ales Stones, dated at about 800 BC, is a remarkable monument in the form of a 67 m long stone-ship. It records the four main solar turning points of the year, the 12 months of the year, each month covering 30 days, except for month 7 which had 35 days (making a full year of 365 days), and the time of the day at 16 points representing 1.5 hour. Ales Stones are built after the same basic geometry as Stonehenge in England.

Link

Journal of Archaeological Science
Volume 40, Issue 1, January 2013, Pages 291–304

Moving metals or indigenous mining? Provenancing Scandinavian Bronze Age artefacts by lead isotopes and trace elements

Johan Ling et al.

The aim of this study is to further the discussion as to whether copper was extracted locally or imported to Sweden during the Bronze Age or if both of these practices could have coexisted. For this purpose, we have carried out lead isotope and chemical analyses of 33 bronze items, dated between 1600BC and 700BC. Among these are the famous Fröslunda shields and the large scrap hoard from Bräckan and other items from three regions in southern Sweden which are also renowned for their richness in copper ores. It is obvious from a comparison that the element and lead isotope compositions of the studied bronze items diverge greatly from those of spatially associated copper ores. Nor is there any good resemblance with other ores from Scandinavia, and it is concluded that the copper in these items must have been imported from elsewhere. The results furthermore indicate that there are variations in metal supply that are related to chronology, in agreement with other artefacts from Scandinavia as well as from other parts of Europe. Altogether these circumstances open up for a discussion regarding Scandinavia’s role in the maritime networks during the Bronze Age.

Link

November 27, 2012

Skull trauma in Neolithic Scandinavia

I would be interested to know how this Neolithic sample might differ from more recent ones. My limited understanding suggests that between-male violence often has a signalling component whereby an individual's or group's dominance over another is asserted, so the fight often does not go all the way to death, but only until the status quo is manifested by the controlling party or toppled by a challenger.

This type of "signalling" aspect of violent behavior does not apply to male-to-female violence because of the physical strength inequality between the sexes. Indeed, as with violence towards children or the elderly, male-to-female violence may have a "reverse signalling" effect, because it suggests that the perpetrator is unable to fight with "the strong" and is only able to assert physical dominance in "easy fights". On the other hand, such "easy fights" might be more abundant if perpetrators tend to enter fights they can win.

Fight-to-the-death, on the other hand, may occur either by accident (e.g., when the aim is to assert dominance, but the killer underestimates the tolerance of the victim), or by intent (when the aim is physical annihilation, either because reconciliation with the victim is perceived to be impossible, or because the victim's death may help keep other challengers in check).

There may be lots to learn about gender roles and social hierarchy from large palaeoanthropological samples. For example, how much did ideology affect secular patterns of interpersonal violence, and how much did changes in weapon technology (e.g., from Neolithic to Bronze, Iron, and more recently firearms).

Am J Phys Anthropol DOI: 10.1002/ajpa.22192

Patterns of violence-related skull trauma in neolithic southern scandinavia

Linda Fibiger et al.

This article examines evidence for violence as reflected in skull injuries in 378 individuals from Neolithic Denmark and Sweden (3,900–1,700 BC). It is the first large-scale crossregional study of skull trauma in southern Scandinavia, documenting skeletal evidence of violence at a population level. We also investigate the widely assumed hypothesis that Neolithic violence is male-dominated and results in primarily male injuries and fatalities. Considering crude prevalence and prevalence for individual bones of the skull allows for a more comprehensive understanding of interpersonal violence in the region, which is characterized by endemic levels of mostly nonlethal violence that affected both men and women. Crude prevalence for skull trauma reaches 9.4% in the Swedish and 16.9% in the Danish sample, whereas element-based prevalence varies between 6.2% for the right frontal and 0.6% for the left maxilla, with higher figures in the Danish sample. Significantly more males are affected by healed injuries but perimortem injuries affect males and females equally. These results suggest habitual male involvement in nonfatal violence but similar risks for both sexes for sustaining fatal injuries. In the Danish sample, a bias toward front and left-side injuries and right-side injuries in females support this scenario of differential involvement in habitual interpersonal violence, suggesting gendered differences in active engagement in conflict. It highlights the importance of large-scale studies for investigating the scale and context of violence in early agricultural societies, and the existence of varied regional patterns for overall injury prevalence as well as gendered differences in violence-related injuries.

Link

November 26, 2012

Medieval signal of Swedish (?) admixture in Finland

I took the FIN (Finnish), GBR (British), and CDX (Chinese Dai) samples of the 1000 Genomes Project, each of which has a sample size of 100 in order to investigate the signal of East-West Eurasian admixture in Finns. While neither Britons nor Dai could be imagine of having contributed to Finns directly, they ought to make useful proxies of a NW European population lacking recent East Eurasian ancestry, and an East Eurasian population lacking recent West Eurasian ancestry respectively.

In the following, I will assume a generation length of 29 years and a sample birthyear of 1980 as in previous experiments.

First, the 1-reference analysis of FIN using GBR produced an admixture proportion lower bound of 37.4 +/- 5.1 percent.

The corresponding analysis of FIN using CDX produced an admixture proportion lower bound of 4.4 +/- 1.0 percent.

The 2-ref admixture test with {GBR,CDX} reported success:

Test SUCCEEDS (z=2.76, p=0.0057) for FIN with {GBR, CDX} weights
But, the decay rates were inconsistent, a situation which might occur when major admixture from different sources took place at different times. In particular, the one using CDX corresponded to 65.57 +/- 8.36 generations, and the one using GBR to 25.48 +/- 4.93 generations.

In calendar dates, Finns are estimated to have mixed with an East Eurasian CDX-like population between 170BC-320AD and with a NW European GBR-like population between 1100-1380AD.

The central date of the latter estimate is 1,240AD, which corresponds quite closely to the beginning of Swedish rule and is in the middle of the 13th. century, between the time when Finland was initially claimed for western Christendom (12th c.) and the time when the conflict between Sweden and Russia was settled (14th c.).

October 29, 2012

Assessment of ancient European DNA with 'globe13'

Here is my assessment of ancient DNA from Europe using the globe13 calculator:


You can consult the spreadsheet for the distribution of these components in modern populations. As in previous analyses, the main distinction is between Northern European-like Mesolithic population (Ajv52, Ajv70, and Bra1), and Mediterranean-like Neolithic (Oetzi and Gok4) one.

October 23, 2012

Ancient European DNA assessment with 'globe10'

I had previously assessed the same using globe4. See post on globe10 and associated spreadsheet.


The results appear similar to previous analyses overall, with the main features being the presence of "Southern" in Neolithic farmers (which peaks in the Near East), and its absence in hunter-gatherers. Some of the "Amerindian"-like admixture that was evident in globe4 has been "absorbed" by the Atlantic_Baltic (main European) component, but it is interesting that the Swedish hunter-gatherers (Ajv52/Ajv70) continue to show some Amerindian as well as other eastern (Australasian/South Asian) admixture that is lacking in the other samples. These individuals are outside the range of modern populations, but they overall tend to map to the most similar Atlantic_Baltic component with the addition of some eastern influences.

Also of interest is the fact the Oetzi is the only sample which shows a slice of West Asian (5.7%) admixture in this analysis. This was also the case in the previous one using K7b (1.4%). Gok4, on the other hand, the fellow Neolithic individual from Sweden seems to lack this. The arrangement of the Big Three West Eurasian components (Southern/West Asian/Atlantic_Baltic) has subtly changed in this calculator, but it would be tempting, nonetheless, to see in the little West Asian admixture that Oetzi has but Gok4 and the Mesolithic samples seem to lack, something of the vanguard of the arrival of the West Asian component in Europe. Obviously more samples are needed, including ones from the most interesting regions of the Balkans and Anatolia.

October 21, 2012

Ancient European DNA assessment with 'globe4'

In a previous experiment, I showed that ADMIXTURE at K=4 tracks the same signal of Amerindian-like admixture detected with f-statistics. I encapsulated that analysis in the globe4 calculator over at the Dodecad Project blog, and decided to use it to assess a few ancient European autosomal samples:


Please note that a very variable number of SNPs was extracted from these various samples. These results should be viewed as indicative of possible patterns that might be confirmed by a more thorough analysis. Also, please consult the globe4 post for more details on the methodology behind it, and the interpretation of the 4 components.

With these various caveats, I would say that these results seem to make some sense and to be fairly consistent with the scenario of Patterson et al. (2012):

  • Oetzi and Gok4, the "farmers" seem to lack the Amerindian component
  • Ajv52, and Ajv70, the northern hunter-gatherers seem to possess it
  • Bra1, the Mesolithic Iberian seems to lack it as well
Bra1 also happens to be the most limited sample in terms of available SNPs. Nonetheless, this would appear broadly consistent with the idea that the "Amerindian"-like admixture in Europeans emanated from north-eastern Europe. Today, all continental Europeans seem to possess some of it, but this can be explained by migration of Ajv-like individuals and their mixtures into Western and Southern Europe from central or northern Europe for which there is ample historical and archaeological evidence (e.g., Italo-Celts, Germans, and Slavs, in addition to other, earlier phenomena).

A broader context

The absence of the Amerindian-like admixture in South Indian Brahmins and Armenians, and its paucity Kurds and Iranians might indicate that this type of ancestry was not represented in ancient Armenians and Indo-Iranians. Indeed, all these populations possess less of this admixture than those of the North Caucasus. Cypriots possess none of it as well, where the Greek_D sample, a small 2.5% portion. In a previous analysis, I estimated a historical-era estimate of North European admixture in Greeks, and this admixture presumably incorporates the signal of Amerindian-like admixture. Additionally, an Iron Age individual from Bulgaria will soon be announced as being Sardinian-like.

The sum of these factors leads me to believe that the signal of Amerindian-like admixture did not play an important role in the formation of the Graeco-Phrygians (and their Armenian relatives) and the Indo-Iranians, or at least did so to an insignificant degree. As the former expanded westward from the PIE homeland, and the latter eastward, they would have had little opportunity to encounter this type of admixture; rather, they would have admixed with Sardinian-like individuals in the west, and Ancestral South Indian (ASI)-like or East Asian individuals in the east.

On the other hand, as Indo-European groups expanded into eastern Europe, setting off a chain of events that would eventually transform most of the northern part of the continent, and, in historical times, much of the rest of it, they would have met with Ajv-like individuals carrying the signal of Amerindian-like admixture, as well as the Oetzi/Sardinian-like farmers that had spread all the way to Scandinavia by the late Neolithic. The population formed by this mixture would have carried with it the signal of Amerindian-like ancestry, and would then transpose it across the continent. The signal would become increasingly muted westward and southward, and indeed this is what we observe.

UPDATE: It is interesting to see that South Indian Brahmins (both the Metspalu et al. sample, and my Iyer_D and Iyengar_D samples) lack this admixture, while Uttar Pradesh Brahmins do not, given the rolloff evidence for a more recent admixture of the latter. This is consistent with a historical admixture event, after the migration of Brahmin groups southwards, as described in that post.

September 11, 2012

West Asian and North European admixture in Basques and Indo-Europeans

In a previous post I showed that Basques are lacking in the West Asian admixture present in all their West European Indo-European neighbors, consistent with my theory of a late Indo-European invasion of Europe whose ultimate source was the highlands of West Asia.

But, there are alternative theories, one of which purports that the Proto-Indo-Europeans were northern Europeoid pastoralists from the eastern European steppe. Since the North_European ancestral component is lacking in the Tyrolean Iceman and Gok4, the TRB Swede, it is conceivable that North_European bearing populations introduced this component during the Indo-European invasion.

Of course, there is absolutely no archaeological evidence for a massive migration out of the steppe into Europe, as even the main proponents of the steppe hypothesis accept, and as physical anthropology makes clear. And, we don't have to invoke an eastern European invasion to explain the North_European component, since it was present among pre-Indo-European hunter-gatherers from both Gotland and Iberia, as two ancient DNA studies have shown.

In any case, I took the HGDP and 1000Genomes European populations, together with the West_Asian and North_European Dodecad components, and calculated f3 statistics of the form:

f3(IE; Basque, Dodecad Component)

where Basque is either HGDP French_Basque or 1000 Genomes Pais_Vasco_1KG, and Dodecad Component is either West_Asian or North_European.

All the results can be found in the spreadsheet.

Again, there is evidence of West Asian+Basque admixture in all Indo-Europeans (|Z| less than -3) except the islanders from Canarias and Orkney, and the Russians; in the latter case, Basques are probably a poor stand-in for their pre-Indo-European ancestry. So, 32 of 38 comparisons are significant.

One would expect such negative f3 statistics to also apply in the North European+Basque case. After all, there are historically known migrations of Northern Europeoids into Western Europe (both Celts as well as Germanics) which did not affect Basques linguistically; moreover, Basques are southern Europeans, and many of the tested populations are northern Europeans, who are expected to turn up as mixtures of North European+Basque. However, a total of 16 of 38 comparisons are significant, involving, as expected mostly northern European populations.

It thus appears that geography and recent history is sufficient to explain the excess of North_European in some populations. Despite having a dataset with an excess of Iberian and North European populations, not many significant f3 statistics appear, and these are mostly as expected.

In conclusion, by comparing Basques vs. Indo-Europeans there appears no good evidence for the theory that Indo-European languages were brought into western Europe by a massive migration of northern Europeoids from eastern Europe. Basques do not appear distinctive in terms of the North_European component, but they do appear distinctive in terms of the West_Asian one.

This confirms previous ADMIXTURE analyses that Basques occupy an "intermediate" position along the north-south axis of variation in Europe, and an absolutely terminal one in terms of the West Asian component.

It is very interesting that ancient DNA research has provided clues about a very "uneven" landscape of prehistoric Europe, with Sardinian-like farmers in Sweden and Northern European-like hunter-gatherers in Iberia and very little in-betweens. But, these two elements eventually did mix, and, with the addition of a new group of people emanating from the highlands of West Asia, acquired their Indo-European speech, and went on to become the living nations of Europe.

Much remains to be discovered: the first ancient DNA traces of the constituent elements must be identified in space and time, and the history of their intermixture must be tracked.

July 09, 2012

Oldest dairying in Sweden from Mälardalen (Funnelbeaker)

Journal of Archaeological Science Available online 5 July 2012

Lipid residue analyses of Early Neolithic funnel-beaker pottery from Skogsmossen, eastern Central Sweden, and the earliest evidence of dairying in Sweden

Sven Isaksson, , Fredrik Hallgren

This study address the question of the use and function of Early Neolithic (4000-3000 cal. BC) funnel-beaker pots from Mälardalen in eastern Central Sweden. The material studied is pottery from a wetland offering at the site Skogsmossen in the province of Västmanland. While deposited under ritual circumstances in a fen, the pots were likely used in a domestic domain on the settlement adjacent to the offering fen, prior to final deposition. The lipid analysis indicate a varied vessel use, there are traces of aquatic resources, plants, terrestrial animals and milk. The identification of milk residue is the oldest so far from Sweden.

Link

June 10, 2012

Assessing Neolithic Europeans with 'weac2'

I have used the West Eurasian cline calculator 'weac2' to assess the Tyrolean Iceman and Neolithic Swedes. The admixture proportions can be seen below, and appear largely consistent with all previous analyses of the same individuals:


It is interesting that Gok4, the Swedish Megalithic TRB female belongs to the Atlantic_Baltic and Near_East components, while the two major Y-chromosome haplogroups associated with West European Neolithic sites so far are I2a1 and G2a (Treilles and Dolmen of La Pierre Fritte) whose distribution very well parallels these two components: Atlantic_Baltic/I2a1 in Europe, and Near_East/G2a in the Near East.

The simplest explanation, based on the available evidence, is that the Neolithic populations of Europe were descended from G2a-bearing pioneers entering Europe from the southeast, and encountering an I2a1-bearing population of pre-farmers in Europe itself. The high frequency of I2a1 in Sardinia, as well as the presence of G2a in that population serves to underscore the substantial genetic continuity between ancient Neolithic Europeans and modern Sardinians.

The absence of the South_Asian component in 'weac2' in all of these individuals is also important. This component captures ancestry (both Caucasoid and Ancestral South Indian) from further east and south, where both G2a/I2a1 are quite rare. As I have noted before, both Europe and South Asia have been affected in late/post-Neolithic times by migrations from West Asia.

It is tempting to associate this population movement with the spread of Indo-European languages, and we can only eagerly await more autosomal ancient DNA samples that will reveal the arrival of the "missing components" over the Neolithic substratum.

April 30, 2012

Another look at Neolithic inhabitants of Sweden, using 'euro7'

After my initial analysis of the new Swedish Neolithic data, I decided -like with the Iceman-  to assess them with the euro7 calculator. Check the spreadsheet for comparative values in modern populations.

Of the hunter-gatherers: Ajv70 turns out to be 100% "Northeastern" in this analysis; Ajv52 is 75.1% "Northeastern", 21.8% "Northwestern", 2.9% "Far_Asian", and 0.3% "African". The "Northeastern" component is modal in the Baltic area.

Gok4, the Megalithic farmer was 61.5% "Northwestern", 21.4% "Southeastern", and 17.1% "Southwestern". The "Northwestern" component is modal in Atlantic Europe.

Modern Scandinavians have very little "Southeastern" and "Southwestern" by comparison, and this is probably what accounts for the clear southern origin of Gok4. But, Gok4 does seem to share the major "Northwestern" component with modern Scandinavians.

Two additional 'euro7' components occur in modern Scandinavians, "Caucasus" (~5%) and "Northeastern" (~20-25%). These components also occur in modern populations of the British Isles: the "Caucasus" one at similar or higher frequencies, the "Northeastern" one at lower ones than is the case in Scandinavia.

The fact that these two 'euro7' components are also missing in Oetzi strongly suggests to me that there was a late-Neolithic or post-Neolithic east-to-west migration into Europe from an eastern source area. Given the absence of "Caucasus" in Neolithic Gotland hunter-gatherers, it is a reasonable assumption that this migration may have originated from further south and east, where the "Caucasus" component occurs in modern populations.

There have been several indications linking Northwestern Europe with the Northeast Caucasus region. The latter exhibits high levels of Y-haplogroup R1b, the main Northwest European lineage. It also exhibits unexpectedly high levels of the "Northwest" component. I have little doubt that these twin facts constrain our understanding of the peopling of Western Europe by anchoring it -in some manner- to the Caspian and its environs.

If I had to guess I would propose the following scenario:
  • The "Northwestern" component represents the pre-Megalithic first farmers of Northwestern Europe, consisting of Linearbandkeramik farmers emanating from Central Europe and admixing with pre-farming Atlantic hunter-gatherers.
  • The "Megalithic" phase of the Neolithic saw the infusion of a new wave of maritime colonists originating in the eastern Mediterranean ("Southeastern") via Iberia ("Southwestern") and reaching their terminus in Scandinavia.
  • The last major population movement into Northwestern Europe involved the arrival of a population element from the northern parts of the Near East via the Caucasus, probably originating in the north Iran/Armenia/Azerbaijan/Dagestan "short arc" west and south of the Caspian where there is a local maximum of R1b frequency.
Thankfully, there is ongoing ancient DNA work on both the European steppe and the Balkans/Anatolia, i.e., the two possible conduits through which any additional "players" in the peopling of Europe must have passed through. Together with ancient DNA study of other archaeological cultures in continental Europe itself, (e.g., Corded Ware/Bell Beaker) our picture of prehistoric events is bound to become ever sharper in coming years.And, hopefully, once the actors in the drama are revealed, we can move on to the late Bronze and Iron Ages, to see how they interacted to form the historical peoples of West Eurasia.

April 28, 2012

A first look at the DNA of Neolithic inhabitants from Sweden

I was eager to get my hands on the ancient DNA from ancient Swedish Neolithic people, as soon as I became aware of it a few months ago. I was finally able to extract SNPs from the data, and I decided to test the samples with my K7b and K12b calculators from the Dodecad Project, as I had also recently done for the Tyrolean Iceman. You can skip to the Results section if you want.

I extracted the following number of SNPs from the different individuals, that were in common with my main HGDP reference:

  • 15,734 SNPs: Gok4 (TRB / farmer)
  • 15,385 SNPs: Ajv52 (PWC / hunter-gatherer)
  • 25,108 SNPs: Ajv70 (PWC / hunter-gatherer)
I did have some trouble with my code for extracting data from the third hunter-gatherer individual, Ire8. This also happens to have the lower number of SNPs as reported by Skoglund et al. so its non-inclusion is probably not a great loss.

K7b and K12b are based on a set of 166,770 SNPs, so I intersected the SNPs of the ancient individuals with them, resulting in:

  • 4,054 SNPs: Gok4
  • 4,077 SNPs: Ajv52
  • 6,631 SNPs: Ajv70
This is, of course, a small number of SNPs, and if we tried to infer structure within West Eurasia with them, we might fail. Nonetheless, by exploiting the structure inferred by the larger number of SNPs in modern populations, and using these to test the ancestry of the ancient ones, we get results that appear to agree fairly well with Skoglund et al. (2012).

A problem with comparing against extant populations, rather than ancestral components is that relationships are averaged: for example, Turks in Skoglund et al. appear quite distant to both Neolithic groups, but we cannot know to what extent this is due to their small levels of central/east Eurasian ancestry and to what extent this is due to their native Anatolian ancestry.

We now have two ancient autosomal DNA sampling locations, and both turned up unexpected results. The Iceman, a Copper Age inhabitant of the Alps resembled modern Sardinians. A Megalithic Swedish farmer resembled Southern Europeans, while his hunter-gatherer contemporaries were outside the range of modern variation. These results should give us caution about the identity of past populations elsewhere. 

As I have argued elsewhere, the past seems to have been much more dynamic than many had suspected, and the people that walked and rowed to the ends of the Earth during the Upper Paleolithic did not suddenly grow fetters or decided to stay put during the Neolithic as many "Paleolithic continuity" adepts had proposed.

A couple more caveats:

  1. Irrespective of their actual origin, these individuals would still be inferred to be some admixture of the ancestral components adding up to 100%. This hints at their affiliations, but does not -in itself- supply evidence of their absolute proximity to the ancestral components.
  2. As more and more ancient individuals are sampled, we will be able to generate genuine ancient populations that are ancestral to modern ones. When that happens, we can directly test modern individuals against panels of ancient ones. For the time being, we have to make do with the reverse, i.e., test ancient individuals against panels of modern ones.


RESULTS


In all comparisons with other K7b results, you should take into account the much smaller number of SNPs used on the Neolithic remains from Sweden.

The K7b results are below. Consult the spreadsheet for comparative values in modern populations.


The K12b results are below. Consult the spreadsheet for comparative values in modern populations.

The raw percentages can be seen below; I have also added the results previously calculated for Oetzi, the Tyrolean Iceman:



DISCUSSION


The results for the two hunter-gatherer samples are as expected predominantly "Atlantic_Baltic" at K=7 and "North_European" at K=12. Since these two samples are outside modern variation, it is expected that their mapping may have added noise; see this post about the dangers lurking at the edges of variation.

Nonetheless, the results can be interpreted as reflecting the fact that the "Atlantic_Baltic" and "North_European" components partially reflect the pre-farming population of Europe. At K=12 it is noteworthy that there is a minor "Atlantic_Mediterranean" admixture in the two hunter-gatherer samples. In my opinion, this may reflect either some level of admixture with the incoming farmers and/or the pre-farming component (but of Western European rather than Baltic type) that may also exist in these foragers. On balance, however, the "North_European" component far outweighs the "Atlantic_Mediterranean" one, which is also consistent with their location (Gotland) which ties them to the Baltic rather than Atlantic Europe.

The farmer sample is remarkable in that, like the Tyrolean Iceman, she seems to be made up entirely of "Atlantic_Baltic" and "Southern" at K=7. There is a hint that the order of the two components are reversed in Gok4 relative to Oetzi, which probably makes sense. The third major West Eurasian component at this level of resolution, the "West Asian" one is conspicuously absent. This component -bimodal in the Caucasus and Balochistan, and strongly represented in the highlands of West Asia in between the two- does occur at ~10% in modern Northern Europeans, so its absence in all Neolithic samples so far hints at its later introduction into at least parts of Europe.

The result at K=12 is fascinating, since Gok4 turns out to be 81% "Atlantic_Mediterranean", and, like Oetzi, with a noticeable "Southwest_Asian" strain. The "Atlantic_Mediterranean" component is bimodal in modern Sardinians and Basques, while the "Southwest_Asian" radiates from southern parts of the Near East into Mediterranean Europe.

Gok4 appears to be "even more Atlantic_Mediterranean" than any modern population. As I mention in the original post, the inhabitants of megalithic monuments  of North-Western Europe were believed by Coon to belong to a "Long Barrow type" which he considered ancestral to the modern "Atlanto-Mediterranean" type. Here is his description:
Toward the end of the Neolithic period, the western Mediterranean countries were invaded by seafarers of a tall, exceptionally long-headed Mediterranean variety; some of these invaders passed through the Straits of Gibraltar, whence they also invaded the British Isles and Scandinavia. 
I would say that the evidence is not incompatible with this scenario. We must probably wait to see whether Gok4 was descended from seafarers from the eastern Mediterranean (where the "Southern" component is modal), following the Mediterranean and then Atlantic coasts up to Scandinavia, or whether they are descended from a different group of people who followed the plains and river valleys of the Balkans and Central Europe and arrived to the north via the inland route. The strong Atlantic_Mediterranean result, coupled with high levels of allele sharing in Cyprus, Greece, France, and the Netherlands, but not particularly in the northern Balkans leads me to prefer the maritime colonization scenario, at least for now. Ancient DNA from more European regions will hopefully help us better understand "what really happened in prehistory."

April 26, 2012

Ancient DNA from Neolithic Sweden (Skoglund et al. 2012)

A new paper in Science solidifies the case for migration as the cause for the diffusion of agriculture in Europe. Discontinuity between early Neolithic farmers and Mesolithic foragers in Central Europe had provided strong hints about this discontinuity, and these were confirmed by other ancient European DNA, e.g., from Treilles, or the Tyrolean Iceman. The case now appears irrefutable, that people not ideas were involved in the spread farming to the northern fringes of Europe.

If we were to ever find signs of acculturation, the north-eastern corner of Europe may be best place to look for it. Agriculture arrived late to Scandinavia and the Baltic, so there was maximum opportunity for Neolithic groups in the area to acquire pre-Neolithic genes from acculturated farmers during their ~2ky long journey from the Aegean. Conversely, forager populations persisted here longer than elsewhere in Europe, both due to the remoteness of the area and the relative unsuitability of the Neolithic package brought from more southern latitudes.

During the Neolithic period there still existed foragers in Scandinavia who belonged to the Pitted Ware (PWC) culture. These have been the object of a previous mtDNA study, which found them to be strongly differentiated from contemporaneous Funnel Beaker or Trichterbecherkultur (TRB) farmers. The latter were farmers who were also associated with Megalithic monuments in northern Europe.

A recent article by Rowley-Conwy (2011), from which the figure on the left is taken, gives some archaeological perspective on the Neolithic of southern Scandinavia:
This farming spread must have been by boat. There were no native aurochs on Zealand (Aaris-Sorensen 1980), so the early cattle at Akonge were definitely imported. Farther north, agriculture was probably carried by boat up the coasts, an easier method of travel than overland (see above). Baltic crossings would require longer open-water voyages than in the Cardial or LBK. Irish curraghs can, however, make substantial voyages and weather considerable seas (Hornell 1938, sec. 5:17–21), and a large one has even crossed the Atlantic (Severin 1978).

...

The agricultural arrival in southern Scandinavia thus appears sharp. Gradualist views of Late Mesolithic developments can be discounted despite the spread of shoe-last axes beyond the farming frontier. Western Norway presents a similar pattern: axes and ceramics were in circulation for over a millennium beyond the farming boundary.
This was the dusk of the European foragers: whatever their contribution to subsequent European populations, their way of life would soon give way to that of the farmer and shepherd. The Pitted Ware culture can indeed be seen as their "last stand", the last time in prehistory when they could co-exist on fairly equal terms with their farmer neighbors.

Hence, it is very exciting to be able to study DNA from this place and time directly, as Skoglund et al. do in a new paper which reports the successful extraction and analysis of ancient DNA from 3 PWC hunter-gathers and one TRB farmer of about ~5,000 years ago:
The Neolithic farmer sample ('Gok4') was excavated from a megalithic burial structure in Gokhem parish, Sweden, and has been directly 14C-dated to 4,921 ± 50 calibrated years BP (calBP), similar to the age (5,100-4,900 calBP) of the majority of other finds in the area (15). There were no indications from the burial context suggesting that Gok4 was different from other TRB individuals (15, 16), and strontium isotope analyses indicate that Gok4 was born less than 100 km from the megalithic structure, similar to all other analyzed TRB individuals from the area (17). The three Neolithic hunter-gatherer samples were excavated from burial grounds with single inhumation graves on the island of Gotland, Sweden, for which associated remains have been dated to 5300-4400 calBP (16).
We must keep in mind that a limited amount of DNA sequence was extracted, which corresponds to a few tens of thousands of SNPs in common with the best modern SNP set used; this corresponds to ~5% of the genome, with different success rates for the four sampled individuals. We must also not forget that these are farmers and foragers from a single point in space-time, and from the periphery of Europe, so we should be cautious in generalizing about the Neolithic transition in other parts of Europe.

Nonetheless, the new study reveals two important pieces of information:

First, the 3 PWC individuals are strongly differentiated from the single TRB one:
Regardless of the underlying model, our study provides direct genomic evidence of stratification between Neolithic cultural groups separated by less than 400 km, differentiation which encapsulates the extremes of modern-day Europe, and appears to have been largely intact for ~1,000 years after the arrival of agriculture.
So, it appears that these individuals lived at roughly the same time and within a small area of Europe, and yet they are as different from each other as the most distant current European populations are. These were not simply drawn from the same or similar populations, some of them deciding to take up farming while others to practice fishing and hunting. These were different populations who maintained their distinctiveness long after "first contact".

Two models have dominated European prehistory in recent decades: acculturationists claimed that the Neolithic package of domesticated plants and animals was transmitted across the continent while the people largely stayed put, while demic diffusionists claimed that people did move, but -at least in the most popular version of the model- that they gradually intermarried with local hunter-gatherers, forming a genetic cline of ancestry, at the far end of which the farmers were mostly derived from local foragers.

One could very well say that the acculturationist model views prehistoric people as smart folk with no legs, apparently ready to take up a good new idea, but reluctant to leave their birthplace. The demic diffusionist model, on the other hand, viewed them as mindless automata, moving across the landscape with little purpose, marrying who they met, and filling a continent in much the same way that gas molecules end up filling a room into which they are introduced.

Both these models are now revealed to be wrong: rather, it seems that "leapfrog" colonization may be responsible for the spread of agriculture and its associated technologies (such as Megalithism) across Europe. In this model, farmers lept from place to place across the landscape intentionally, preserving their gene pool and largely ignoring the pre-existing foragers of the landscape.

Of course, farmer and hunter eventually did mix, and hunting cultures became extinct. But, this was a process that seems to have been complete after 4,000 years BP. Acculturation did eventually happen, and agriculturalists did eventually diffuse to every corner of Europe. But, these are events that happened after the initial group(s) of pioneers had opened the frontier. In this respect, the colonization of Europe bears some resemblance to the settlement of the Americas by Europeans: it happened by leaps and bounds, and the early waves of explorers and pioneers may have opened the landscape but did not immediately fill it: this happened later as a result of demographic growth and new waves of migration, with the extant populations being differentially descended -in different proportions- from migrants and natives.

The second important point of the new study is the revelation that the single Neolithic individual from northernmost Europe was similar to extant southern Europeans:
To more closely investigate the genetic similarity of extant European populations (22, 24) to Neolithic humans, we determined for each SNP and each extant population the average frequency of the particular allele found in either the Neolithic hunter-gatherers or the Neolithic farmer (16). The Neolithic hunter-gatherers shared most alleles with Northern Europeans, and the lowest allele sharing was with populations from Southeastern Europe (Fig. 3A). In contrast, the Neolithic farmer shared the greatest fraction of alleles with Southeastern European populations (Cypriots and Greeks), and showed a pattern of decreasing genetic similarity for populations from the Northwest and Northeast extremes of Europe (Fig. 3B). Individuals from Turkey stand out by low levels of allele sharing with both Neolithic groups, possibly due to gene flow from outside of Europe, but all other European populations can roughly be represented as a cline where allele sharing with Neolithic hunter-gatherers is negatively correlated with allele sharing with Neolithic farmers (Fig. 3C). 
Panel C from the allele sharing figure (left) suggests why we should be cautious about trying to reconstruct European prehistory on the basis of a simple 2-way model of admixture between farmers and hunters.

It is true that extant European populations do fall on a clear cline between them that is strongly significant (R=-0.58, p=0.0029). This means is that they are different to each other in the same ways that farmers/hunters were different from each other. But, this still leaves about 2/3 of the variance unexplained: this may be partly due to the "noise" added by the small number of SNPs, and partly by the contribution of other ancestral groups to extant variation. One of these groups may be the east Eurasian element which must contribute to the differentiation of Turks from Europeans. But, there were probably other West Eurasian elements not represented by the two Neolithic groups: the Mesolithic Pitted Ware individuals have been previously assigned predominantly to mtDNA haplogroup U, which forms a minority in extant Europeans; and a handful of Neolithic samples (LBK, Oetzi, Treilles) have failed to turn up any signs of the dominant R1 Y-haplogroup of extant Northern Europeans. There must be other actors to be revealed in the unfolding story of European origins.

A strong hint for this can also be found in the quite unexpectedly low "TRB" allele sharing of groups from the Northwestern Balkans. This is quite unexpected, as the area is widely believed to be a conduit through which agriculture spread into Central Europe. It is also an area with world maxima of Y-haplogroup I, a lineage which may be a remnant of Paleolithic Europeans, and correspondingly low levels of haplogroups that appear to have arrived later into Europe.

Another important point is that levels of allele sharing between these Neolithic individuals and modern Europeans is generally lower than between most pairs of modern European populations. This is, in part, expected, since the Neolithic specimens are separated by modern populations by ~5ky of evolution, but may also be due to the contribution of unsampled groups to the ancestry of the latter.

From the paper:
We found that compared to a worldwide set of 1,638 individuals (21-23), all four Neolithic individuals clustered within European variation (Fig. S5). However, when focusing the analysis on 505 individuals of European and Levantine descent, the three Neolithic hunterg atherers appeared largely outside the distribution of the modern sample, but in the vicinity of Finnish and northern European individuals (Fig. 1A). In contrast, the Neolithic farmer clustered with southern Europeans, but was differentiated from Levantine individuals. This general pattern persisted for a geographically broader reference data set of 1,466 extant individuals of European ancestry (22, 24) (Fig. 1B), for a much larger number of markers from 241 individuals in the 1000 genomes project (25) (Fig. 1C), and using model-based clustering (26, 27) (Fig. 1D). Although all Neolithic individuals were excavated in Sweden, neither the Neolithic farmer nor the Neolithic hunter-gatherers appeared to cluster specifically within Swedish variation, a pattern that remained also for a larger sample of 1,525 individuals from across Sweden (28) (Fig. S9, Fig.S21-22).
I will try to perform an analysis of these 4 Neolithic Europeans, as I did with the Iceman, and see how they relate to a larger number of populations: for example, the Mesolithic hunter-gatherers have the highest allele sharing with Poles: do they share even more with Lithuanians and other Baltic peoples? The Neolithic farmer is by far closer to Cypriots: are there any populations of the Near East that are close to it as well?

Hopefully, in the near future we may get our first glimpses of genuine Mesolithic Europeans:
In our genomic analyses, the Scandinavian Neolithic hunter-gatherers (PWC) have a genetic profile that is not fully represented by any sampled contemporary population (Fig. 1), and may thus constitute a gene pool that is no longer intact or that no longer exists. While the origin of the Neolithic hunter-gatherers is contentious, the similar mtDNA haplogroup composition of PWC individuals (8) (Table 1) and Mesolithic- and Paleolithic individuals (7, 29) indicate some continuity with earlier European populations, but resolving this hypothesis will require pre-Neolithic genomic data.
The continuity between Mesolithic and Neolithic hunter-gatherer populations in the Baltic is supported by craniometric analysis from a recent paper (left), but it is definitely worth investigating whether -despite their strong differentiation- the Neolithic farmers and foragers of Sweden may not have already started -at least partially- the process of amalgamation.

Hopefully we can soon extract more DNA from other Neolithic Europeans, as well as pre-contact European foragers. It is probably in the Copper and Bronze Ages that we are to encounter some the remaining players that formed the European genetic landscape and witness how they all combined to form the proto-historical and recent Europeans.

A Postscript:

Until recently, it had become commonplace in archaeology to seek local origins for most archaeological phenomena. Three years ago, I pointed out that new evidence was pointing towards a major migrationism comeback in our understanding of European prehistory. So, it is worth reviewing what was once thought about the people buried in Swedish megalithic monuments. From Carleton Coon's The Races of Europe, (1936) Chapter IV):
In Sweden, out of twenty-four male crania found in passage graves, only one was brachycephalic; for the most part a pure Long Barrow type is represented. (Section 12) 
The Megalithic Long Barrow people must have come by sea, and they probably came from somewhere in the Mediterranean. (Section 10)
The paper is also discussed in the weekly Science podcast. The supplementary materials are freely available.


Science 27 April 2012: Vol. 336 no. 6080 pp. 466-469 DOI: 10.1126/science.1216304

Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe

Pontus Skoglund1,*, Helena Malmström1, Maanasa Raghavan2, Jan Storå3, Per Hall4, Eske Willerslev2, M. Thomas P. Gilbert2, Anders Götherström1,5,*,†, Mattias Jakobsson

The farming way of life originated in the Near East some 11,000 years ago and had reached most of the European continent 5000 years later. However, the impact of the agricultural revolution on demography and patterns of genomic variation in Europe remains unknown. We obtained 249 million base pairs of genomic DNA from ~5000-year-old remains of three hunter-gatherers and one farmer excavated in Scandinavia and find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.

Link

March 24, 2012

Report on the symposium on Modern Human Genetic Variation

Joshua Akey summarizes the talks of a recent symposium at the Swedish Royal Academy of Sciences. Two bits of information stand out from his report. The first:

In another talk focused on demography, Mattias Jakobsson (Uppsala University, Sweden) presented novel data on the impact of the agricultural revolution on the genetics of contemporary European populations. Specifically, Jakobsson and colleagues obtained nearly 250 Mb of sequence from three 5,000-year-old remains of Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia. Analysis of these sequences in the context of the present day European gene pool suggests that the spread of agriculture involved the northward migrations of farmers. Thus, these data provide the most direct and compelling support for the demic diffusion model of agriculture (as opposed to cultural diffusion) described to date. 

It seems I have my answer to the what's next question. Jakobsson has been doing some interesting work on the demography of human emergence and dispersal, so it will be interesting to see not only the novel sequences from these Neolithic Scandinavians, but also how they fit into existing models of demic diffusion.

The second bit of information:

Similarly, Jeff Wall (University of California San Francisco, USA) described a novel method for inferring archaic admixture, which he applied to publicly available whole-genome sequence data generated by Complete Genomics. Provocatively, he finds higher rates of introgression in Asians compared to Europeans. An advantage of Wall’s method is that it does not require an archaic genome to infer introgression, and thus he was able to also test the hypothesis that contemporary African genomes have signatures of gene flow with archaic human ancestors. Strikingly, Wall indeed did find evidence of archaic admixture in African genomes, suggesting that modest amounts of gene flow were widespread throughout time and space during the evolution of anatomically modern humans.

I guess that I shouldn't throw explanation #1 out the window yet. Wall was involved in the recent paper on archaic African admixture, which only looked at a small subset of the genome, so it is nice to see that he is now working with full genomes, and that the race to data mine complete genomes for archaic admixture is afoot.

The book of abstracts is online at the symposium site. The Jakobsson paper does seem to agree with our emerging picture of a non-local origin of northern European farmers as well as greater survival of pre-farming populations in the northern periphery of Europe, but it will be interesting to see where exactly extant populations fall on the farmer-hunter/gatherer continuum.
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Northern Europe 
Mattias Jakobsson
Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden 
The prehistoric spread of farming in Europe has garnered intense interest for almost a century, and was one of the first questions to which population genetic data was used to investigate demographic hypotheses. However, the impact of the agricultural revolution on the European gene pool remains largely unknown. We obtained 249 million base pairs of quality-filtered human autosomal sequence data from some 5,000 year-old remains of three Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia, the northernmost fringe of agricultural practice at the time. Applying novel methods to study population structure based on low genome-coverage data, we find that Northern European Neolithic farmers are most similar to modern-day southern Europeans, contrasting sharply to Neolithic hunter-gatherers who are most similar to extant individuals from northern Europe. With most extant European populations appearing genetically intermediate between the two Neolithic groups, our results suggest that migration from the south by a genetically distinct group of humans accompanied the spread of agriculture to geographic regions where hunting and gathering was the mode of subsistence, but that admixture eventually shaped modern-day patterns of genomic variation.

Archaic admixture in the human genome 
Jeff D Wall
Department of Epidemiology & Biostatistics, University of California, San Francisco, USA 
We describe a method that uses patterns of linkage disequilibrium in extant human populations to identify regions of the genome that were inherited from ‘archaic’ human ancestors, such as Neandertals, Homo erectus or H. floresiensis. We validate this approach using two recently published archaic human genomes, and show that several ancient admixture events must have occurred, both within and outside of Africa. We also explore differences in the amount of archaic admixture across different contemporary human populations.


Finally, here is the meeting report:

Investigative Genetics 2012, 3:7 doi:10.1186/2041-2223-3-7

Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation 

Joshua M Akey

Link (pdf)

August 05, 2011

Genetic structure of Swedish population


PLoS ONE 6(8): e22547. doi:10.1371/journal.pone.0022547

The Genetic Structure of the Swedish Population

Keith Humphreys et al.

Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise Fst) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions.

Link

May 24, 2011

Finding the founder of Stockholm

Birger and his son belonged to Y-haplogroup I1 and had haplogroup H and Z1a mtDNA respectively. The presence of Z1a is interesting, suggesting that occasional Asian mtDNA sequences in Swedes may have been present in that population from a fairly early historical period. The female had mtDNA U5b1.

The authors also tested for the lactase persistence allele: Birger was heterozygous, and the other two individuals had the T (persistent) allele.

The Y-chromosome results will be added to the Ancient Y-chromosome studies page.

Annals of Anatomy - Anatomischer Anzeiger
doi:10.1016/j.aanat.2011.03.014

Finding the founder of Stockholm – A kinship study based on Y-chromosomal, autosomal and mitochondrial DNA

Helena Malmström et al.

Historical records claim that Birger Magnusson (died 1266), famous regent of Sweden and the founder of Stockholm, was buried in Varnhem Abbey in Västergötland. After being lost for centuries, his putative grave was rediscovered during restoration work in the 1920s. Morphological analyses of the three individuals in the grave concluded that the older male, the female and the younger male found in the grave were likely to be Birger, his second wife Mechtild of Holstein and his son Erik from a previous marriage. More recent evaluations of the data from the 1920s seriously questioned these conclusions, ultimately leading to the reopening and reexamination of the grave in 2002. Ancient DNA-analyses were performed to investigate if the relationship between the three individuals matched what we would expect if the individuals were Birger, Erik and Mechtild. We used pyrosequencing of Y-chromosomal and autosomal SNPs and compared the results with haplogroup frequencies of modern Swedes to investigate paternal relations. Possible maternal kinship was investigated by deep FLX-sequencing of overlapping mtDNA amplicons. The authenticity of the sequences was examined using data from independent extractions, massive clonal data, the c-statistics, and real-time quantitative data. We show that the males carry the same Y-chromosomal haplogroup and thus we cannot reject a father–son type of relation. Further, as shown by the mtDNA analyses, none of the individuals are maternally related. We conclude that the graves indeed belong to Birger, Erik and Mechtild, or to three individuals with the exact same kind of biological relatedness.

Link

February 10, 2011

Swedish population structure (Salmela et al. 2011)

From the paper:
In our earlier study [4], we saw that North European populations exhibited differing amounts of IBS similarity to East Asians so that Finns, especially Eastern Finns, were the most similar. Now we have observed the same phenomenon - though in a smaller degree - within Sweden, where Norrland showed the most of East Asian similarity and Götaland the least. This is consistent with earlier Y-chromosomal studies [13]. In strong contrast, however, neither Norrland nor Eastern Finns showed any increase in similarity to the Vologda Russians, and a similar lack of affinity between Finns and Russians can also be seen in separate datasets [6], [13]. Thus, if the current references are representative of Russians in this respect, the observed affinity to Eastern Asia would not be mediated by contacts with Russians but could reflect an ancient eastern influence predating the arrival of Slavic populations to Northeastern Europe in the end of the first millennium [23]. It remains unclear whether the eastern affinity observed in Sweden would date back to the same era, or rather reflect the amount of later Finnish contacts to the area.


PLoS ONE 6(2): e16747. doi:10.1371/journal.pone.0016747

Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data

Elina Salmela et al.

Abstract

The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (FST = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.

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