More Y-chromosome super-fathers

The time estimates are based on a mutation rate of 1x10-9 mutations/bp/year which is ~1/3 higher than mutation rate of Karmin et al.  So the values on the table may be a little lower.

There may be additional founders with recent time depths than shown in the table, e.g., a very shallow clusters within E-M35 (probably E-V13?) and a couple of shallow clusters within I-P215

Also of interest is the fact that Greeks and Anatolian Turks do not show evidence of the recent Y-chromosomal bottleneck:

The plots are consistent with patterns seen in the relative numbers of singletons, described above, in that the Saami and Palestinians show markedly different demographic histories compared with the rest, featuring very recent reductions, while the Turks and Greeks show evidence of general expansion, with increased growth rate around 14 KYA. A different pattern is seen in the remaining majority (13/17) of populations, which share remarkably similar histories featuring a minimum effective population size ~2.1–4.2 KYA (considering the 95% confidence intervals (CIs) reported in Supplementary Table 4), followed by expansion to the present.

Related:

• Y chromosome super-fathers 
• Bottleneck in human Y-chromosomes in the last 10,000 years

Nature Communications 6, Article number: 7152 doi:10.1038/ncomms8152

Large-scale recent expansion of European patrilineages shown by population resequencing

Chiara Batini, Pille Hallast et al.

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Link

Craniofacial morphology of Greeks through 4,000 years

Anthropol Anz. 2014;71(3):237-57.

Craniofacial morphology in ancient and modern Greeks through 4,000 years.

Papagrigorakis MJ, Kousoulis AA, Synodinos PN. Abstract

BACKGROUND:

Multiple 20th century studies have speculated on the anthropological similarities of the modern inhabitants of Greece with their ancient predecessors. The present investigation attempts to add to this knowledge by comparing the craniofacial configuration of 141 ancient (dating around 2,000-500 BC) and 240 modern Greek skulls (the largest material among relevant national studies).

METHOD:

Skulls were grouped in age at death, sex, era and geographical categories; lateral cephalograms were taken and 53 variables were measured and correlated statistically. The craniofacial measurements and measurements of the basic quadrilateral and cranial polygon were compared in various groups using basic statistical methods, one-way ANOVA and assessment of the correlation matrices.

OBSERVATIONS:

Most of the measurements for both sexes combined followed an akin pattern in ancient and modern Greek skulls. Moreover, sketching and comparing the outline of the skull and upper face, we observed a clock-wise movement. The present study confirms that the morphological pattern of Greek skulls, as it changed during thousands of years, kept some characteristics unchanged, with others undergoing logical modifications.

CONCLUSION:

The analysis of our results allows us to believe that the influence upon the craniofacial complex of the various known factors, including genetic or environmental alterations, is apt to alter its form to adapt to new conditions. Even though 4,000 years seems too narrow a span to provoke evolutionary insights using conventional geometric morphometrics, the full presentation of our results makes up a useful atlas of solid data. Interpreted with caution, the craniofacial morphology in modern and ancient Greeks indicates elements of ethnic group continuation within the unavoidable multicultural mixtures.

Link

The Mediterranean route into Europe (Paschou et al. 2014)

An interesting new (open access) paper in PNAS includes some new data from Crete, the Dodecanese, Cappadocia, and several other Greek (and a few non-Greek) populations, and proposes that the Neolithic followed an island-hopping migration into Europe. This is a study on modern populations that nicely complements the recent ancient mtDNA paper from PPNB which found an affinity to Neolithic Near Eastern populations among the modern inhabitants of Cyprus and Crete.

It is hard to imagine that there were ever any major impediments to gene flow between Anatolia and the Balkans as the Aegean islands and Hellespont are not formidable barriers to any culture with even rudimentary technology. Hopefully in the future it will become possible to look at ancient DNA from Greece and Anatolia and directly determine how the transfer of the Neolithic package into Europe took place and how much of the ancestry of modern populations stems from the Neolithic inhabitants vs. more recent shuffling of genes in either direction.

The authors also computed f3-statistics to see if populations were admixed, but found no significant evidence for it. If, for example, Dodecanesians were intermediate between mainland Greece and Anatolia they might have a negative f3(Dodecanesian; Cappadocia, Peloponnese) statistic. A negative statistic proves admixture but a positive one does not disprove it, but, in any case, there is no signal of admixture here so the results are compatible with the authors' model and probably incompatible with a recent admixture that would leave a significant negative signal (i.e., Dodecanesians/Cretans would have intermediate allele frequencies between Cappadocians and mainland Greeks).

PNAS doi: 10.1073/pnas.1320811111

Maritime route of colonization of Europe

Peristera Paschou et al.

The Neolithic populations, which colonized Europe approximately 9,000 y ago, presumably migrated from Near East to Anatolia and from there to Central Europe through Thrace and the Balkans. An alternative route would have been island hopping across the Southern European coast. To test this hypothesis, we analyzed genome-wide DNA polymorphisms on populations bordering the Mediterranean coast and from Anatolia and mainland Europe. We observe a striking structure correlating genes with geography around the Mediterranean Sea with characteristic east to west clines of gene flow. Using population network analysis, we also find that the gene flow from Anatolia to Europe was through Dodecanese, Crete, and the Southern European coast, compatible with the hypothesis that a maritime coastal route was mainly used for the migration of Neolithic farmers to Europe.

Link

Human admixture common in human history (Hellenthal et al. 2014)

A string of recent papers argued for admixture in human populations at time scales from the Middle Pleistocene to recent centuries. A new paper in Science makes the point convincingly for extensive admixture in humans over the last few thousand years. The authors include the creators of Chromopainter/fineStructure software; the new "Globetrotter" method appears to be a natural extension of that method that seemed to work wonderfully well except for the limitation of producing only a tree of the studied populations.

The paper has a companion website in which you can look up the admixture history of individual populations.

While reading this study, it is important to remember its limitations. Two are immediately obvious: (i) admixture events can only be detected for the last few thousand years, as this method depends on pattern of linkage disequilibrium which decays exponentially with time due to recombination, and (ii) detection of admixture seems to depend on the presence of maximally differentiated populations from the edges of the human geographical range; for example, the Japanese appear unadmixed even though they are clearly of dual Jomon/Yayoi ancestry. On the other hand, the method does detect the admixture present in the San at a similar time scale.

The case of Northwestern Europe appears especially striking as none of the populations from the region show evidence of admixture. This may be because the mixtures taking place there (e.g., between "Celts" and "Anglo-Saxons" in Great Britain) involved populations that were not strongly differentiated. Alternatively, population admixture history may have preceded the last few thousand years and is thus beyond the temporal scope of this method.

An exception to the rule that populations at the edges of the human range appear to be unadmixed are the Armenians who appear to be the only * between the Atlantic and Pacific in Figure 2D (shown at the beginning of this post). The companion site lists their status as "uncertain".

Other results are more questionable; for example, the authors assert that Sardinians are an admixed population with one side being "Egyptian-like" and the other "French-like" whereas the ancient DNA evidence as it stands would rather indicate that Sardinians are the best approximation of Neolithic Europeans currently in existence and so are more likely to (mostly) possess a gene pool that traces back to ~8-9 thousand years in Europe. It will be quite the surprise if so many Europeans from 5kya or earlier look like modern Sardinians and ancient Sardinians don't!

The analysis of Eastern Europe is particularly interesting as it documents three way admixture (Northern/Southern/NE Asian) in most populations but two way admixture (Northern/Southern) in Greeks, estimated at ~37%. The authors claim that this is related to the Slavs, which seems reasonable given the 1,054AD age estimate. On the other hand, according to the companion website, the southern element in Greeks is inferred to be Cypriot-like and it's far from clear that the pre-Slavic population of Greece was Cypriot-like or indeed represented by any of the populations in the authors' dataset.

The three-way admixture in much of eastern Europe is not particularly surprising as history furnishes ample evidence for groups of steppe origin in the region during historical times. Some bequeathed their both language and name (e.g., Magyars), others only their name (e.g., Bulgarians) on the local Europeans, but records indicate a widespread presence of "eastern" groups in Europe from the time of the Huns to that of the Ottomans. A study of late Antique eastern Europeans from the Baltic to the Aegean may help better document how the twin phenomena of the eastern invasions and the spread of the Slavs shaped the present-day genetic diversity of the region.

I suspect that a few ancient samples will be far more informative for understanding the recent history of our species than the most sophisticated modeling of modern populations. Nonetheless, it's great to have a new method that maximizes what can be learned about the past from the messy palimpsest of the present.

Science 14 February 2014: Vol. 343 no. 6172 pp. 747-751 DOI: 10.1126/science.1243518

A Genetic Atlas of Human Admixture History

Garrett Hellenthal et al.

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

Link

The place of Armenian in the Indo-European language family

Journal of Language Relationship • Вопросы языкового родства • 10 (2013) • Pp. 85—137

The place of Armenian in the Indo-European language family: the relationship with Greek and Indo-Iranian*

Hrach Martirosyan

The main purpose of this paper is to present lexical correspondences that unite Armenian with Greek and/or Indo-Iranian. They include shared innovations on the one hand, and isolated lexemes on the other. These two lexical corpora — lexical innovations on an inherited basis and isolated words — can be placed within the same temporal and spatial framework. After the Indo-European dispersal Proto-Armenian would have continued to come into contact with genetically related Indo-European dialects. Simultaneously, it would certainly also have been in contact with neighbouring non-Indo-European languages. A word can be of a substrate origin if it is characterized by: (1) limited geographical distribution; (2) unusual phonology and word formation; (3) characteristic semantics. The material presented here, albeit not exhaustive, allows to preliminarily conclude that Armenian, Greek, (Phrygian) and Indo-Iranian were dialectally close to each other. Within this hypothetical dialect group, Proto-Armenian was situated between Proto-Greek (to the west) and Proto-Indo-Iranian (to the east). The Indo-Iranians then moved eastwards, while the Proto-Armenians and Proto-Greeks remained in a common geographical region for a long period and developed numerous shared innovations. At a later stage, together or independently, they borrowed a large number of words from the Mediterranean / Pontic substrate language(s), mostly cultural and agricultural words, as well as animal and plant designations. On the other hand, Armenian shows a considerable number of lexical correspondences with European branches of the Indo-European language family, a large portion of which too should be explained in terms of substrate rather than Indo-European heritage.

Link (pdf)

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

Y chromosome study of Italy (Brisighelli et al. 2012) incl. sample of Greek speakers from Salento

This is a wonderful new source of information on Y-chromosome variation in Italy, that also includes some samples of the linguistic minorities of Ladins and Griko speakers.

The latter is particularly interesting to me, because, these last Greeks of Magna Graecia are descended either from the ancient colonists or medieval Eastern Roman settlers, and as such may represent a group of Greek descendants that (i) may have admixed to some extent with local Italic speakers, but (ii) will not have had an opportunity to experience much post-medieval gene flow that may have affected Greeks from the Aegean.

There may be something wrong with the presentation of the haplogroup frequencies on the left; in particular, based on the text, I think that what appears as R1* is in fact R1*(xR1a1).

In any case, here are my observations on the Grecani Salentini sample:

• They, as well as the Messapi, possess the highest frequencies of E-M78. This ties them to the Balkans in a very obvious way; this haplogroup was also interpreted as a signal of Greek colonization in Sicily and Massalia. This seems like the most obvious explanation; note that Salento is in Messapia, so the high frequency in the non-Greek denizens of the region may be simply the result of language shift, since the remaining Greek speakers are presumably the last remnant of a once much more numerous population that was linguistically Italicized as have most other Greek speaking populations of Italy and Sicily.
• Their highest frequency haplogroups are R1*(xR1a1) and J2. Both are fairly common haplogroups in both Greece and Italy, so only a fine-scale analysis would be able to differentiate between what might be pre-Greek and what is Greek in origin. In any case, I have proposed that these two haplogroups were typical of (albeit not limited to) the Graeco-Phrygo-Armenian clade, so their occurrence in this sample is not surprising.
• There is an occurrence of I*(xM26) chromosomes. This requires finer phylogenetic resolution, but certainly the absence of M26 -which has a SW European distribution- is interesting to note.
• Haplogroup G-M201 again requires finer-scale resolution, and could be anything from a relative of the Neolithic Italians (having been found in the Tyrolean Iceman) to much more recent events.
• Within haplogroup J, the majority of the chromosomes belong to clade J2, with about a tenth of the frequency made up of J*(xM62, M172). Note that these are not necessarily J*(xJ1,J2) as indicated in the figure, since M62 defines only a part of the J1 lineage.
• The absence of haplogroup R1a1 in this sample is perhaps the most interesting finding. This occurs at a frequency of ~10% in Greek samples from Greece and is fairly variable. I have previously observed that it was absent in the south stream of Indo-European based on its paucity in Armenians, Albanians, and its uneven distribution in Greeks. Its absence in the Italian Griko sample reinforces this idea. A caveat, however, is that the origin of the Greek settlement of Italy can be traced to southern Greece and western Anatolia, so it's still possible that some R1a1 was present in other areas of the Aegean basin since pre-medieval times.

The authors of the paper use many conventional labels of what is "Neolithic" and what is not (e.g., R1*(xR1a1) is claimed as Mesolithic). But, certainly, both age estimation of modern chromosomes (e.g., Wei et al. 2012) and the ancient Y chromosome studies cast doubt on this association. I would say that rather than being predominantly pre-Neolithic, it might appear that the Y-chromosome gene pool of Italy may have been formed in late Neolithic to medieval times, with the only lineages that can convincingly trace their ancestry to the Neolithic or earlier epochs being G and I-M26.

As for the Ladins, the high frequency (67.7%) of R1*(xR1a1) is consistent with what I believe to have been the main Italo-Celtic lineage.

Finally, I should point out the occurrence of a couple of haplogroup L samples; this haplogroup is more typical of populations much to the east, being the "eastern" cousin of the more "western" haplogroup T within the LT clade. Certainly a finer-scale resolution of these two L samples might be informative about their potential origins and/or the ancient distribution of this rather mysterious haplogroup.

PLoS ONE 7(12): e50794. doi:10.1371/journal.pone.0050794

Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage

Francesca Brisighelli et al.

Abstract
Background

According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country.

Methods/Principal Findings

A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers.

Conclusions/Significance

Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

Link

Differences and similarities between Greek and European HapMap populations

Not surprisingly, TSI captued Greek genomic structure better than CEU did, although not always:

The TSI outperform the CEU as reference for the Greek population in 10 regions. However, there are four regions where the CEU are actually better reference samples than the TSI, contrary to what one might expect based on geographic proximity of the populations. Among them, the most notable are a region of chromosome 7 (100% coverage using the CEU as reference vs. 91.7% using the TSI as reference) and the chromosomal region around COMT (100% coverage using the CEU as reference vs. 93% coverage using the TSI as reference). The Chromosome 7 region spans the TAS2R38 gene (responsible for the PTC taster/nontaster phenotype), as well as the CLEC5A gene. The latter gene has been found to have a role in immune response and interact with dengue virus. Finally, the SLC44A5 regions (discussed in previous sections as one of the most population-differentiating regions in our study) were also captured more accurately in Greeks when the CEU were used as the reference population as opposed to the TSI.

Annals of Human Genetics DOI: 10.1111/j.1469-1809.2012.00730.x

Exploring Genomic Structure Differences and Similarities between the Greek and European HapMap Populations: Implications for Association Studies

Vasileios Stathias et al.

Studies of the genomic structure of the Greek population and Southeastern Europe are limited, despite the central position of the area as a gateway for human migrations into Europe. HapMap has provided a unique tool for the analysis of human genetic variation. Europe is represented by the CEU (Northwestern Europe) and the TSI populations (Tuscan Italians from Southern Europe), which serve as reference for the design of genetic association studies. Furthermore, genetic association findings are often transferred to unstudied populations. Although initial studies support the fact that the CEU can, in general, be used as reference for the selection of tagging SNPs in European populations, this has not been extensively studied across Europe. We set out to explore the genomic structure of the Greek population (56 individuals) and compare it to the HapMap TSI and CEU populations. We studied 1112 SNPs (27 regions, 13 chromosomes). Although the HapMap European populations are, in general, a good reference for the Greek population, regions of population differentiation do exist and results should not be light-heartedly generalized. We conclude that, perhaps due to the individual evolutionary history of each genomic region, geographic proximity is not always a perfect guide for selecting a reference population for an unstudied population.

Link

rolloff analysis of Greeks as Sardinian+Brahui

In a previous experiment, I showed that Greeks can be seen as composites of two alternate sets: either a Sardinia-South Asia mix, or a North European-Near East mix. I first studied the latter, which provided a historical-period estimate for the admixture time. I now turn to the former, and use Sardinians and Brahui as parental populations. This complements previous analyses on Armenians and French using similar reference populations. Since I used the Balochi and Burusho in the two previous experiments, I decided this time to use the Brahui, which is the third population which presents a significant f3(Greek; Sardinian, Brahui) signal along the Europe-West Asia axis.

473,174 SNPs were used in total. The exponential fit can be seen below.

The jackknife estimate is 132.890 +/- 35.527 generations, or 3,850 +/- 1030 years. This spans the entirety of the Helladic period, with the mean being close to two often-cited dates for the "coming of the Greeks", corresponding to the destructions at the EHIII/MH boundary (c. 2100BC), and the spread of "Minyan ware" at c. 1900BC, although an earlier or later date is certainly possible.

(An alternative interpretation would relate the earliest Greeks to a Sardinian-like European population and the Asian component to a Luwian-like Anatolian population responsible for the well-known -nth and -ss toponyms in the Aegean.)

A signal of West Asian admixture during the Bronze is certainly consistent with my musings on the spread of metallurgy from the east during this time.

rolloff analysis of North European admixture in Greeks.

One of the signals of admixture in my recent post on the Greeks on the crossroads of Eurasia was between north European and Near Eastern populations, with several pairs of such populations showing a significant negative f3(Greek_D; North European, Near Eastern) statistic. I used rolloff to estimate the date of this admixture.

Note that rolloff assumes a pulse model of admixture, whereby the two populations mix at a point in time, rather than experience gene flow over a protracted period. This may not be applicable in the case of Greeks, since gene flow may have occurred repeatedly throughout history. Also, rolloff estimates admixture times in the absence of very accurate ancestral populations, by exploiting allele frequency differences between them. So, for the first example below, with Finnish_D and Yemen_Jews as reference populations, which showed the most negative f3 statistic, this does not mean that Greeks are the product of admixture between Finns and Yemen Jews, but rather that allele frequency differences between these two populations reflect a contrast between North Europeans and Near Eastern populations, which may, presumably map, to the west Eurasian cline of diminishing Near Eastern "Neolithic" ancestry.

This experiment was performed on a set of 292,223 SNPs, and using the Rutgers map for Illumina chips. The first plot is using Finnish_D and Yemen_Jews as references. The fit does not visually appear extremely convincing, perhaps due to a smaller number of SNPs, or to the aforementioned deviation from the pulse admixture model.

(NB: I used the expfit.sh script with default parameters to do the exponential fit/plotting; note that negative weighted correlation points are not visible in the produced output)

The jackknife estimate of this admixture is 87.849 +/- 20.254 generations, or, assuming a generation length of 29 years, into 2,550 +/- 590 years.

The second plot uses Polish_D and Saudis as references:

The jackknife gives 67.235 +/- 22.148 generations, or 1950 +/- 640 years. The fit seems to capture the rise of the exponential for smaller cM genetic distances reasonably well.

Recently, Graham and Coop used fastIBD to identify a signal of possible Slavic admixture in the Balkans dating to the medieval period, using a similar generation time of 30 years. That method uses shared IBD segments between populations, so it may be limited to uncovering the most recent signal of admixture. Another piece of evidence comes from an abstract in ASHG 2012, according to which an Iron Age individual from Bulgaria was Sardinian-like. Since the Iron Age starts at the conclusion of the 2nd millennium BC, it might seem that a northern European element -whether present or not- had not admixed yet with the people who lived in the Balkans at the time. This seems to parallel the situation in two other earlier locations (c. 5ka in the Tyrolean Iceman and Gok4 Swedish TRB farmer), in which the North_European component was absent, although we cannot yet exclude its absence from the Iron Age Bulgarian, since a little such admixture might still leave an individual mostly Sardinian-like. Finally, levels of the North_European component in Greek individuals seem fairly variable, and this might indicate that levels of this element of ancestry had not had sufficient time to even out in the population.

(A different possibility is that the admixture signal reflects admixture of a Near Eastern kind. I consider this less likely, since there is evidence of "Southern" and "Southwest Asian" ancestry (in the K7b/K12b sense) already in Neolithic Europe.)

More research on the issue is certainly needed, but a first reading of the evidence suggests that this type of admixture may reflect events that took place during the historical period of Greek history.

Each of these experiments took about 1.5 days to complete. I am currently running another set of experiments with ~2-fold more SNPs, and assuming that finishes in good time, I may re-visit the question addressed in this post, to see if standard errors decrease and/or time estimates change with denser coverage.

Greeks on the crossroads of Eurasia

I used the qp3Pop program of ADMIXTOOLS which implements a 3-population test of admixture (Patterson et al. 2012), using Greek_D as a target population and any pair of other populations as possible parental populations. My dataset is similar to that used for the K7b/K12b, but includes all the new data that has accumulated since those tools were released. The number of SNPs is 186,241, and I have also limited the analysis to 115 populations with 10+ individuals.

For more details on the f3 statistic, you should really read the linked paper. Briefly, you should remember the following:

1. Significant negative f3 statistics indicate that the target population and the two parentals do not form a simple tree, but are related in a complex way
2. Positive f3 statistics are consistent with either a simple tree or a history of admixture followed by genetic drift
3. It is not necessary for the parental populations to be themselves unadmixed

The full set of results can be seen in the spreadsheet.

Below you can see the 30 most negative f3 statistics.

The first thing that immediately jumps out is that Sardinians participate in most of these comparisons. And, given the mounting evidence for a Sardinian-like population in prehistoric Europe, including the Balkans, it does appear likely that a Sardinian-like element in the ancestry of Greeks is quite possible.

A different element that is paired up with Sardinians in the most negative f3 statistics consists of a variety of South Asian populations; these comparisons appear stronger than the Sardinian+East Asian ones. This dataset does not include Amerindian populations, for which the effect was strongest in the Patterson et al. paper. I suspect that South Asian populations give out stronger f3 statistics than East Asian ones, because South Asians are composed of a West Asian-like element and an Ancestral South Indian element which is related to East Eurasians. So, South Asians appear as a parental population on account of both the East Eurasian-shift effect observed by Patterson et al., as well as the West Asian-shift effect I've described in a few posts such as this.

A third set of significant comparisons involve Northern Europeans vs. Near Eastern populations, with extrema in the Baltic area and Arabia, which seems to correspond quite well with what I've called the "West Eurasian cline", with populations of northeastern Europe likely possessing a higher degree of continuity with the Mesolithic hunter-gatherers.

Overall, this exercise has convinced me that 2-way admixture models do not capture the complexity of Eurasian prehistory. The Greek population appears intermediate on a number of different clines, the two most important ones being between Sardinia and far Asia and between the Baltic and the Near East.

I will probably repeat this experiment with other populations from this set. I will also probably try to get some admixture dates using as many SNPs as possible, although rolloff appears to have fairly long running times, so I am not sure how practical that will be.

fastIBD analysis of several Jewish and non-Jewish groups

This is more of a "just the data" kind of post, inspired by the two recent papers on Jewish origins. A few quick points:

• fastIBD was run with default parameters over a dataset of 512 individuals/264,539 SNPs
• fastIBD identifies segments of relatively recent origin that are shared by individuals. These results should not be construed as measures of overall genetic similarity or origins. Rather, they suggest which populations have exchanged genes in the relative recent past, say, the last two thousand years or so.
• I included all Ashkenazi_D and North_African_Jews_D samples; of the other Dodecad and reference populations, I took random samples of 10 each; running time of fastIBD increases with the square of the number of individuals, so doing this allowed me to run this in less than a day as opposed to about a week.

With that said, you can get:

• Spreadsheet of numeric results, showing sharing (in centi-Morgans, cM)
• Population-level graphical results, showing an ordering of other populations based on mean IBD sharing.

The following heat map allows for a quick appraisal of populations sharing an excess of IBD sharing (read row-by-row)



And, here are a couple of the visualizations for a few Jewish populations:

Note that all sources of data are listed on the bottom left of the Dodecad blog.

The social network of the Iliad is highly realistic

From the paper:

In an attempt to place the three mythological networks on the spectrum from the real to the fictitious, we compared their properties to actual and imaginary social networks. Table 2 summarises the broad properties of the different types of networks. Of the three myths, the network of characters in the Iliad has properties most similar to those of real social networks. It has a power-law degree distribution (with an exponential cut-off), is small world, assortative, vulnerable to targeted attack and is structurally balanced. This similarity perhaps reflects the archaeological evidence supporting the historicity of some of the events of the Iliad.

arXiv:1205.4324v2 [physics.soc-ph]

Universal Properties of Mythological Networks

Pádraig Mac Carron, Ralph Kenna

(Submitted on 19 May 2012 (v1), last revised 18 Jul 2012 (this version, v2))

As in statistical physics, the concept of universality plays an important, albeit qualitative, role in the field of comparative mythology. Here we apply statistical mechanical tools to analyse the networks underlying three iconic mythological narratives with a view to identifying common and distinguishing quantitative features. Of the three narratives, an Anglo-Saxon and a Greek text are mostly believed by antiquarians to be partly historically based while the third, an Irish epic, is often considered to be fictional. Here we show that network analysis is able to discriminate real from imaginary social networks and place mythological narratives on the spectrum between them. Moreover, the perceived artificiality of the Irish narrative can be traced back to anomalous features associated with six characters. Considering these as amalgams of several entities or proxies, renders the plausibility of the Irish text comparable to the others from a network-theoretic point of view.

Link

Anthropological Investigation of the S. Greece population’s composition in the Bronze Age

Here is a link to S. K. Manolis's 1991 dissertation which complements the previous one by G. Panagiaris, since it includes data from the Peloponnese and Crete. I might translate parts of it in the space below. The author seems to argue for an environmental cause of brachycephalization during the Bronze Age; personally I think that the more likely explanation is intrusion by mountain-folk from either the Pindos area or Anatolia, associated with metallurgy. In any case, I am hopeful that some of the Ancient Greek osteological material, some of which has been excavated many decades ago may still possess usable DNA that could be exploited in future studies that may overcome the limits of craniometry.

A physico-anthropological study of skeletal material from Neolithic age to Hellenistic times in Central Greece and surrounding region

I have located the text of George Panagiaris important 1993 doctoral thesis on Greek skeletal material. This may be one of the most comprehensive efforts to study the Ancient Greek population from a physical anthropological perspective (413 male and 354 female crania, using 65 biometric characters as well odontological traits).

Panagiaris' conclusions in English can be found in p.10 of the document. He confirms that the greater period of discontinuity in the material is observed during the Helladic period (=Bronze Age in Greek archaeology), where broad-headed incoming groups appear, side by side with the older Mediterranean population. He attributes this to the arrival of such people from the highlands Pindos range, although he sees the possibility of Anatolian influences as well, but has no comparative data. He cites the tendency for broader skulls in higher latitudes, although this general trend in H. sapiens probably does not explain the local trend within Caucasoids where the key difference is between mountaineers (where the Alpine, Dinaric, Armenoid, and Pamir-Ferghana types are well-represented) and lowland folk. Perhaps, if various ancient DNA projects manage to study some Greek material we may be able to ascertain the events that were taking place in Greece at that time.


Of course, the issue cannot be seen in isolation, because at this time we see an increase in brachycephalic types in Crete and Anatolia, the appearance of the intrusive brachycephalic Bell Beaker folk in Western Europe, and perhaps even the presence of the interfluvial type (Pamir-Ferghana type) in the eastern Saka. 

Personally, I see something important in these developments: why would broad-headed mountaineers make their appearance in the lowlands at this time in history? I am strongly leaning towards the idea that this has to do with metallurgical innovation during this time. According to Roberts et al. (2009), from which the figure on the left is taken:

Metallurgy in Eurasia originated in Southwest Asia due to the widespread adoption of, and experimentation in, pyrotechnology and the desire for new materials to serve as aesthetic visual displays of identity, whether of a social, cultural or ideological nature. This can be demonstrated through the early use of metal for jewellery and the use of ore-based pigments along with the continued use of stone, bone, and other materials for most tools. The subsequent appearance of metals throughout Eurasia is due to the acquisition of metal objects by individuals and communities re-inventing traditions of adornment, even in regions hundreds of kilometres from the nearest sources of native metals or ores. The movement of communities possessing metallurgical expertise to new ore sources and into supportive societies led to the gradual transmission of metallurgy across the Eurasian landmass. By the second millennium BC, metallurgy had spread across Eurasia, becoming firmly rooted in virtually all inhabitable areas (Sherratt 2006). The ability to smelt different ores, create different metals or increase metal production did not occur in a linear evolutionary fashion throughout Eurasia, but rather appeared sporadically over a vast area – a result of regional innovations and societal desires and demands. 

There is no evidence to suggest that metallurgy was independently invented in any part of Eurasia beyond Southwest Asia. The process of metallurgical transmission and innovation created a mosaic of (frequently diverse) metallurgical traditions distinguished by form, composition and production techniques. It is within this context that innovations such as the earliest working of gold in the Balkans or the sudden emergence of distinctive tin-bronze working in Southeast Asia should be seen. 

The richest ore deposits were found in mountain areas as Thornton (2009) makes clear:

Models for the development of metallurgy in Southwest Asia have for a long time been focussed on research carried out in the lowland regions of the Levant and Mesopotamia. These models do not take into account the different developmental trajectories witnessed in the resource-rich highlands of Anatolia, the Caucasus, and Iran. In this paper, the beginnings of the use and production of metals in Iran will be juxtaposed with a cursory overview of the lowland model (the ‘Levantine Paradigm’) in order to highlight these differences. By synthesizing data from a number of current research projects exploring the early metallurgy of the Iranian Plateau, this paper demonstrates how at least one of the highland regions of Southwest Asia was at the very forefront of technological innovation from the seventh through the second millennium BC.  

I had planned to write a separate post on the interplay between metallurgy and the rise in social complexity that led to the spread of (at least some branches of-) Indo-European and Semitic during time, but this is probably as good a place as any to summarize the argument:

The practice of metallurgy launched the first globalization: in order to produce high quality metal objects, one needed a variety of specialized workers: prospectors, miners, metalworkers. The necessary ores do not occur everywhere on the map, and production requires a complex logistic operation to manage resources and talent. One needed, in addition, to establish a network of traders and warriors to carry out and supervise the trade, since demand for metal objects was wide and not limited to the vicinity of their production.

Production and trade networks facilitated the flow of ideas, and necessitated the flow of peoples, both because expertise was non-local, and also because the producers wanted to supervise their profitable business. There is an advantage to being an early adopter of new technology; many of the shifts in power in world history depended on a technology differential (European guns in the New World, mounted archers on the Eurasian steppe, triremes in the Mediterranean, Macedonian long-spears vs. Persian light infantry being some examples).

The technology differential eventually dissipates as everyone gets access to the new inventions. This process may take several centuries, but in the meantime those monopolizing them enjoy a triple advantage:

1. There is demand for their product
2. They have the better weapons
3. They are part of broader communities that can muster resources against anyone who crosses them

It is no accident that the Bronze Age started with technological innovation and ended up in a series of military conflicts. What began as a transformation of Neolithic communities by monopolizing guilds of the bearers of the new technologies ended up with everyone having access to them, and of course they went to war.

Getting back to the topic of Panagiaris' dissertation, I might try my hand at translating some interesting portions. These will be posted as updates in the space below.

fastIBD over 2,257 Europeans

Razib points me towards a very interesting new paper that applies fastIBD over the large POPRES dataset of Europeans. The most interesting thing about this is that the authors develop techniques for estimating the time depth of the pattern of common ancestry across Europe, and hence are able to conclude that the Slavic expansion has played a bigger role in European history than the Germanic one.

A worthwhile improvement would be to apply a clustering algorithm like I did back in January over the fastIBD output; that way, one does not have to arbitrarily partition Europe into regions, but have the partitions jump out of the data.

A different idea to confirm the scenario presented in this paper would be to drill into different European populations. For example, in the case of the Italians, it would be worthwhile to identify whether there are particular sub-populations with likely Greek or Albanian ancestry who share an excess of IBD with modern Greeks and Albanians.

Population averages may mask such interesting patterns lurking in the data. For example, sub-clusters within populations can be identified with both fineSTRUCTURE and fastIBD, and the corresponding clusters can be assessed with supervised ADMIXTURE to detect how they differ from each other. For example, using this technique, I was able to infer 3 sub-clusters within the ethnic Greek population:

• pop8 (mainland Greek) with ~23% North_European
• pop11 (Greek Cypriot) with ~5% North_European
• pop14 (Cretan, islander, mainland+Asia Minor) with ~12% North_European
• I have also a strong hunch based on a few half Pontic Greek+half mainland Greek data points that unmixed Pontic Greeks would be related to pop22 (Northeastern Anatolia) with ~5% North_European

Based on these results and the fastIBD analysis of Ralph and Coop (the POPRES Greek sample is from northern Greece), it might appear that a hefty portion of the North_European component in Greeks may date to the medieval period, since it is relatively smaller in eastern Greeks and Cypriots and also in the South Italian/Sicilian cluster pop16 of a different analysis, with Italians as a whole lacking the eastern European affiliations of some Greek groups.

Interestingly, ~5% North_European levels would be similar to those of Armenians who are the closest linguistic cousins of the Greeks within the Indo-European family, as well as the the Anatolian Turkish cluster pop13 at ~9%.

Overall, it would appear that some mainland Greek groups received some input as the result of the medieval Slavic intrusions, since the mainland North_European excess appears as a "wedge" within the South Italy/Sicily/Crete/Anatolia/Armenia arc and the fastIBD pattern of sharing suggests that this is due to fairly recent connections.

As I have pointed out before, one limitation of the method of counting shared blocks of ancestry is that it does not disclose the directionality of gene flow. For example, gene flow between Germans and Slavs is detected in this study, which could be ascribed to Germans living in eastern Europe and/or to Slavs becoming acculturated Germans as a result of living within Germanic states or intermarrying with them prior to the age of the nation state.

Finally -and most interestingly- I hope that similar haplotype-based methods can be applied to a wider dataset, because, as it is becoming clear, Europe has not been isolated from Asia or Africa during its long history. The authors mention "Slavic or Hunnic" as an explanation for the pattern of shared ancestry in eastern Europe, but it is only by including Asian groups that we can detect the existence of real Hunnic (or Avar, or Mongol, or Pecheneg, or, ...) ancestry.

Moreover, I am confident that the Bronze Age is well within the power of haplotype-based methods to detect IBD. For example, South Asian populations clearly show differential patterns of affiliation with modern West Eurasian groups, most of which can date to no later than the Bronze Age. Together with the gradual incorporation of the new ancient DNA genomes that are bound to be coming our way soon, it seems that our picture of not only recent history, but also of late prehistory is bound to become much sharper.

arXiv:1207.3815v1 [q-bio.PE]


The geography of recent genetic ancestry across Europe

Peter Ralph, Graham Coop
(Submitted on 16 Jul 2012)

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.

Link

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

First look at Turkish and Kyrgyz data from Hodoğlugil & Mahley (2012)

The authors of the recent paper on Turkish population structure were kind enough to share their data with me. I will be sure to use this data in future experiments, such as the ChromoPainter and fastIBD analysis of Balkans/West Asia, as well as a ChromoPainter analysis of Altaic speakers, following on the footsteps of my recent analysis of Afroasiatic speakers.

PCA


As a first step, after processing the new data, I carried out a PCA analysis (in smartpca with no outlier removal iterations), combined with various Turkic groups, as well as a few neighbors of Anatolian Turks, combining data from the literature and the Dodecad Project.

The Turkic cline from East to West Eurasia, observed by myself and others in various experiments is again evident.

The blowup of the above, focusing on the West Eurasian portion (top right) is easier to read:

As always, population labels are placed in the average position of each population. So, for example, the Behar et al. Iranians_19 sample is shifted to the left, because of the existence of a few African admixed individuals in this sample. The Iranian_D sample of Project participants seem to lack this admixture.

Also, note that since there is no South Asian reference in this first experiment, Iranians overlap with Turks along the first two dimensions. As we've seen in the Dodecad Project, both Iranians and Anatolian Turks are "eastward-shifted" relative to other West Eurasians, but the former have a strong South Asian- and the latter a Central Asian- tendency.

The new Kyrgyz sample falls between the Kazakh and the Altai along the cline, and is more "eastern" compared to the Uygurs and Uzbeks, and more "western" compared to Altai, Tuva, and Dolgans.

Kayseri and Istanbul Turks overlap with Behar et al. Turks as well as the Turkish_D sample. The Aydin sample appears to be more heterogenous, with a more eastern overall center of weight. More on this below.

ADMIXTURE


I also carried out a K=3 ADMIXTURE analysis of the dataset.

Below are the population portraits for the three new Turkish samples, as well as the Kyrgyz sample:

It is obvious that many Turks have low levels of Asian admixture, lacking in their geographical neighbors, but this is quite variable on an individual basis.

UPDATE (17 Feb):


I have also assessed the new data with the K12b calculator. Below are the normalized median proportions.

Y-chromosomes of the Bahamas

I like the line about there being substantially more Y-STR variation in E1b1a7a-U174 and E1b1ba8-U175 in the Bahamas than any African collection. I have argued for years that the central assumption of phylogeography, that the location of highest Y-STR diversity is not necessarily the point of origin of a haplogroup, since Y-STR diversity can be affected both by antiquity and by admixture. Nonetheless, I keep reading papers where tiny differences in Y-STR variation, even if we forget about the noisiness of Y-STRs themselves, are taken as evidence of ancient migrations. Thankfully, the time when Y-STRs were used to infer ancient migrations is over, and the huge collection of Y-STR haplotypes amassed by population geneticists, forensic specialists, and genealogists alike can be put to uses for which it is more amenable.

I can't say I know much about the history of the Bahamas, but this was something I had not heard of before:

Over the last 150 years, the Bahamas has been witness to a varied array of settlers, including Chinese immigrant workers, Greek spongers, Jewish business-men and individuals of Lebanese descent fleeing religious persecution. The extent to which each group has contributed genetically to the Bahamian paternal gene pool, however, is unknown. Our findings suggest that the Greeks, which exhibit relatively high frequencies of haplogroups E1b1b1a*-M78, J2a*-M410, and R1b1b1*-L23 (Semino et al., 2004; Myres et al., 2011), are a likely source of these lineages in the Bahamas, although the presence of M78 derived chromosomes may also signal gene flow from Lebanon (Zalloua et al., 2008). J1e-P58 lineages, on the other hand, which are characteristic of Jewish populations (Hammer et al., 2009) and Arab speaking groups (Chiaroni et al., 2010), may represent genetic signatures of Eastern European Jews and/or Lebanese migrants entering the Bahamas in the early twentieth century.

Another interesting tidbit:

Western European colonialism, although short-lived, appears to have left marked genetic imprints throughout the Bahamian archipelago, with Long Island receiving the strongest European genetic signals and Exuma, the weakest; a distribution pattern consistent with our earlier reports utilizing autosomal STR markers (Simms et al., 2008, 2011). The higher frequency of M269 derived individuals in the Long Island population (55.8%), when compared with the other five Bahamian islands surveyed (ranging from 8.5% to 18.3%), suggests higher gene flow from European males (Saunders, 2003b). According to the 1851 census, Long Island possessed one of the smallest European components (13.1%) yet, by 1953, almost 50% of this population was of ‘‘mixed’’ ancestry (Craton, 1998).

R-M269 seems quintessentially European today, and most living R-M269 men probably have West European ancestry. But, the finding of a high frequency in a Bahamian spot ought to remind us that Y-chromosomes can achieve high frequencies in little time, given the right conditions. Indeed, we can very well draw a parallel between the prehistoric spread of R-M269 into Europe, an event that is still shrouded in mystery, with the late historical movement of the same haplogroup into the Americas. Taking the broad view, these two unrelated events represent two pulses of the same westward spread of a successful Y-chromosome lineage.

It is also nice that scientists are beginning to take notice of very basal Y-chromosomes, going back to Y-chromosome Adam.

Two samples that fell outside of haplogroups B-T (defined by M42) were observed in Abaco (1.5%) and New Providence (0.7%), two Bahamian islands separated by a total of 139.4 km, as well as in a single sample from Haiti (unpublished data). When tested for V171, which, according to Cruciani et al. (2011a) defines the A2-T lineage, all three samples exhibited the ancestral allele. Instead, each individual was derived for the paralogous V152 mutation that determines the A1b lineage. It should be noted that each of the three samples possessed an eight base pair long Poly-T stretch at the M91 locus, indicative of the monophyletic haplogroup A defined by Karafet et al. (2008). However, as a result of the rearrangement of the tree by Cruciani et al. (2011a), haplogroup A no longer represents a monophyletic group, as the A2 and A3 lineages are now united with all haplogroup A lineages other than A1 by their shared possession of V171.

Haplogroup A chromosomes have been collected as isolated examples in many genealogical projects and scientific studies. It's a great idea for someone to take the initiative and collect the most divergent ones, invest in genotyping them fully, and push the boundaries of what we know about the most ancient history of modern human patrilineages.

AJPA DOI: 10.1002/ajpa.21616

Paternal lineages signal distinct genetic contributions from British Loyalists and continental Africans among different Bahamian islands

Tanya M. Simms et al.

Over the past 500 years, the Bahamas has been influenced by a wide array of settlers, some of whom have left marked genetic imprints throughout the archipelago. To assess the extent of each group's genetic contributions, high-resolution Y-chromosome analyses were performed, for the first time, to delineate the patriarchal ancestry of six islands in the Northwest (Abaco and Grand Bahama) and Central (Eleuthera, Exuma, Long Island, and New Providence) Bahamas and their genetic relationships with previously published reference populations. Our results reveal genetic signals emanating primarily from African and European sources, with the predominantly sub-Saharan African and Western European haplogroups E1b1a-M2 and R1b1b1-M269, respectively, accounting for greater than 75% of all Bahamian patrilineages. Surprisingly, we observe notable discrepancies among the six Bahamian populations in their distribution of these lineages, with E1b1a-M2 predominating Y-chromosomes in the collections from Abaco, Exuma, Eleuthera, Grand Bahama, and New Providence, whereas R1b1b1-M269 is found at elevated levels in the Long Island population. Substantial Y-STR haplotype variation within sub-haplogroups E1b1a7a-U174 and E1b1ba8-U175 (greater than any continental African collection) is also noted, possibly indicating genetic influences from a variety of West and Central African groups. Furthermore, differential European genetic contributions in each island (with the exception of Exuma) reflect settlement patterns of the British Loyalists subsequent to the American Revolution.

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