Luwians vs. Hittites and Mycenaeans vs. Luwians

A rather imaginative reconstruction of the events surrounding the Sea Peoples and the ending of the end of the Bronze Age.

Genetic structure of 1,272 Italians

From the paper:

The distribution of the pairwise Fst distances between all population pairs is shown in Supplementary Table S3. The genetic distance between Southern and Northern Italians (Fst=0.0013) is comparable to that between individuals living in different political units (ie, Iberians-Romanians Fst=0.0011; British-French Fst=0.0007), and, interestingly, in >50% of all the possible pairwise comparisons within Europe (Supplementary Figure S7).

European Journal of Human Genetics advance online publication 11 November 2015; doi: 10.1038/ejhg.2015.233

The Italian genome reflects the history of Europe and the Mediterranean basin

Giovanni Fiorito et al.

Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population’s ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., ‘barbarian invasion’ of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe.

Link

Mesolithic monolith from Sicilian Channel

Journal of Archaeological Science: Reports Volume 3, September 2015, Pages 398–407

A submerged monolith in the Sicilian Channel (central Mediterranean Sea): Evidence for Mesolithic human activity

Emanuele Lodolo, Zvi Ben-Avraham

The ancient geography of the Mediterranean Basin was profoundly changed by the increase in sea level following the Last Glacial Maximum. This global event has led to the retreat of the coastlines, especially in lowland areas and shallow shelves, such as the Sicilian Channel. The NW sector of this shelf, known as Adventure Plateau, is studded by isolated shoals mostly composed of Late Miocene carbonate rocks and by some volcanic edifices. These shoals, until at least the Early Holocene, formed an archipelago of several islands separated by stretches of extremely shallow sea. One of these submerged features – the Pantelleria Vecchia Bank – located 60 km south of Sicily, has been extensively surveyed using geophysical and geological methods. It is composed of two main shoals, connected seaward by a rectilinear ridge which encloses an embayment. Here we present morphological evidence, underwater observations, and results of petrographic analysis of a man-made, 12 m long monolith resting on the sea-floor of the embayment at a water depth of 40 m. It is broken into two parts, and has three regular holes: one at its end which passes through from part to part, the others in two of its sides. The monolith is composed of calcirudites of Late Pleistocene age, as determined from radiocarbon measurements conducted on several shell fragments extracted from the rock samples. The same age and composition characterize the metre-size blocks forming the rectilinear ridge. The rest of the rocks composing the shoals are mostly Tortonian limestones–sandstones, as revealed by their fossil content. Extrapolating ages from the local sea level curve, we infer that seawater inundated the inner lands at 9350 ± 200 year B.P., the upper limit which can be reasonably taken for the site abandonment. This discovery provides evidence for a significant Mesolithic human activity in the Sicilian Channel region.

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

Interesting talks @ Penn: Zheng He and Mount Vesuvius

I had recently mentioned Zheng He on account of his Y chromosome.

Great Voyages: Zheng He


Pompeii Lecture Series: Mount Vesuvius in Human History

Climate caused the Late Bronze Age collapse in the Eastern Mediterranean

PLoS ONE 8(8): e71004. doi:10.1371/journal.pone.0071004

Environmental Roots of the Late Bronze Age Crisis

David Kaniewski et al.

The Late Bronze Age world of the Eastern Mediterranean, a rich linkage of Aegean, Egyptian, Syro-Palestinian, and Hittite civilizations, collapsed famously 3200 years ago and has remained one of the mysteries of the ancient world since the event’s retrieval began in the late 19th century AD/CE. Iconic Egyptian bas-reliefs and graphic hieroglyphic and cuneiform texts portray the proximate cause of the collapse as the invasions of the “Peoples-of-the-Sea” at the Nile Delta, the Turkish coast, and down into the heartlands of Syria and Palestine where armies clashed, famine-ravaged cities abandoned, and countrysides depopulated. Here we report palaeoclimate data from Cyprus for the Late Bronze Age crisis, alongside a radiocarbon-based chronology integrating both archaeological and palaeoclimate proxies, which reveal the effects of abrupt climate change-driven famine and causal linkage with the Sea People invasions in Cyprus and Syria. The statistical analysis of proximate and ultimate features of the sequential collapse reveals the relationships of climate-driven famine, sea-borne-invasion, region-wide warfare, and politico-economic collapse, in whose wake new societies and new ideologies were created.

Link

IBD sharing between Iberians and North Africans (Botigué et al. 2013)

An interesting new paper documents an excess of IBD sharing between Iberians (excluding Basques) and North African (and particular NW African) populations.

It would have been nice if the authors had used techniques such as rolloff and ALDER or those of Jin et al. (2012) to say something about the time/nature of the admixture event detected via IBD sharing; insteady, they use variance in admixture proportions, which gives a probably much noisier estimate, with the basic idea being that in the first few generations post-admixture there are individuals with much varying admixture proportions, but these tend to be homogenized over time.

The occurrence of North African-specific admixture in SW Europe has long been suspected on the basis of Y-chromosome/mtDNA work (e.g., the presence of E-M81 which is probably the best North African marker in existence). It also makes sense, because of the limited occurrence of Sub-Saharan markers in Iberia: such elements did not, presumably, fly over North Africa, but landed in Iberia via people who were themselves admixed.

A couple notes of caution:

(i) the use of ADMIXTURE as a means of estimating admixture proportions is dangerous in this case, because of the hybridity of "North Africans" themselves, which according to published estimates experienced Sub-Saharan African admixture in the last few thousand years. In my own experiments it is clear that "North Africans" are a mixture of three basic components related to Europe, Sub-Saharan Africa, and the Near East. Nonetheless, in my own experiments I do also get an excess of the component I've labeled "Northwest African" in Iberia that is not shared by Basques or French.

(ii) as I've emphasized before, IBD sharing between populations does not indicate the direction of gene flow. One would have to look at the ancestry of the shared segments to determine their origin. To give a simple example, an IBD segment shared by a Spaniard and a Mexican could be European, African, or Native American, and -thanks to historical knowledge- we can be fairly sure that the number of such segments is also in the given order.

Given that Iberia is the neighbor of NW Africa one would not be surprised if there was gene flow in both directions, and while North Africa gene flow into Iberia is one possible explanation, some of the gene flow may have gone the other way, e.g., with contacts during the Pax Romana, fleeing Iberian Muslim in the post-reconquista period, Barbary pirates attacking Christian ships and the like. In any case, it would be interesting to catalogue IBD shared segments between Iberia and NW Africa in terms of their geographical origin.

(iii) the sources and timing of admixture could potentially be determined by ancient DNA work. The three most recent time periods are related to the slave trade (both European of Africans and vice versa), the Islamic period, and the Roman Empire. Presumably, with the sampling of enough individuals, that type of admixture ought to manifest in populations living before/after each of these three events.

In any case, this is an interesting paper which is also accompanied by publicly accessible data.

PNAS doi: 10.1073/pnas.1306223110

Gene flow from North Africa contributes to differential human genetic diversity in southern Europe

Laura R. Botigué et al.

Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.

Link

Facial reconstruction of 5,600-year old Maltese woman

Source: Revealed...the face of a Maltese woman 5,600 years ago

Heritage Malta also launched a 3D virtual reconstruction of facial features based on one of the prehistoric skulls (over 5,000 years old) found at the Xaghra Stone Circle in Gozo. It revealed, for the very first time, what one of the earliest Maltese actually looked like.
It was a face which was much closer to what one would expect from a woman of our day and age rather than that of a person who lived on the islands over 5,000 years ago.

Pre-Neolithic Mediterranean Island settlement

PhysOrg coverage of a Science perspective:

Modern science has held that islands such as Cyprus and Crete were first inhabited by seafaring humans approximately 9,000 years ago by agriculturists from the late Neolithic period. Simmons writes that research over the past 20 years has cast doubt on that assumption however and suggests that it might be time to rewrite the history books. He cites evidence such as pieces of obsidian found in a cave in mainland Greece that were found to have come from Melos, an island in the Aegean Sea and were dated at 11,000 years ago as well as artifacts from recent digs on Cyprus that are believed to be from approximately 12,000 years ago. He adds that some researchers have also found evidence that something, or someone caused the extinction of pygmy hippos on Cyprus around the same time.  

Simmons also suggests that the first inhabitants of many of the Mediterranean islands may not have been modern humans at all. Instead, he says evidence has been found that shows that they might have been Neanderthals, or Homo Erectus. Recent excavations on Crete have turned up artifacts that are thought to be 110,000 years old, for example, and a stone axe was found that is believed to have been made on the same island as far back as 170,000 years ago. Since modern humans are believed to have come into being roughly 100,000 to 200,000 years ago, the possibility exists that such artifacts were left behind by an early ancestor or cousin.

Science 16 November 2012: Vol. 338 no. 6109 pp. 895-897 DOI: 10.1126/science.1228880

Mediterranean Island Voyages

Alan Simmons

Some of the classical world's most innovative cultures developed on Mediterranean islands, but their earlier human use is poorly known. The islands, particularly those further from the mainland such as Crete and Cyprus, were thought to have been first colonized about 9000 years ago by late Neolithic agriculturalists with domesticated resources. Until about 20 years ago, claims of earlier, pre-Neolithic occupations on any of the islands did not stand up to critical scrutiny (1), but current investigations are challenging these perceptions. Discoveries on Cyprus, Crete, and some Ionian islands suggest seafaring abilities by pre-Neolithic peoples, perhaps extending back to Neanderthals or even earlier hominins. In Cyprus, Neolithic sites have been documented that are nearly as early as those on the mainland.

Link

Mediterranean ornaments in the Hungarian Neolithic

The use of Spondylus ornaments by European Neolithic cultures is well known, and is one of the characteristics tracking the spread of the Neolithic into Europe. A new study has looked at late Neolithic Hungary, to track the origin of these ornaments, confirming that they did indeed come from the Mediterranean (Adriatic or Aegean), and not the Black Sea or fossil shells from the Carpathian Basin.

Given the evidence that late Neolithic European farmers, even as far north as Sweden were indeed of Mediterranean origin, their continued use of these ornaments possibly reflects a tradition going back to their origins in the Aegean, rather than simply a fashion that spread simply for its decorative properties.

Journal of Archaeological Science, doi:10.1016/j.jas.2012.09.022

Tracing the source of Late Neolithic Spondylus shell ornaments by stable isotope geochemistry and cathodoluminescence microscopy

Bernadett Bajnoczi et al.

Determination of the source of Spondylus objects is essential for the interpretation of Late Neolithic exchange systems and the social role of shell ornaments. We performed stable isotope analysis combined with cathodoluminescence microscopy study on ornaments (beads, bracelets) made of Spondylus shells excavated at the Aszod-Papi foldek archaeological site in Hungary, to define their origin. For comparison Spondylus finds from Neolithic sites of Greece, modern Spondylus shells from the Aegean and the Adriatic, as well as fossil Spondylus and Ostrea shells from the Carpathian Basin were also examined. Oxygen isotope composition of Spondylus finds from Aszod ranges between -1.9 and 2.1 ‰ and overlaps with the oxygen isotope range of shell objects from other Neolithic sites. Modern Spondylus shells from the Aegean and the Adriatic show overlapping δ18O values with one another and with the Neolithic objects; while recent shells of the Black Sea clearly are separate isotopically from the Mediterranean ones and most of archaeological artefacts. Spondylus shells from the Aszod site have Mediterranean origin; their source can be the Aegean or the Adriatic. Based on a former strontium isotope study the use of fossil Spondylus shells is excluded as raw material used for ornaments, however, in recent years the use of fossil shells was reintroduced. The shell ornaments from Aszod-Papi foldek and the fossil oyster shells collected from the Carpathian Basin exhibit some overlapping oxygen isotope values; however, cathodoluminescence microscopy indicates that the Spondylus objects retained their original aragonite material. Diagenetic calcite, which occurs typically in the fossil shells, was not detected in the ornaments suggesting that the studied objects were made of recent shells. Calcitic parts observed in some Spondylus objects are not related to fossilisation.

Link

Archaeometallurgy in the Mediterranean

Continuing a discussion on metallurgical innovation which I began here.

Some interesting excerpts from a book chapter:

Tin bronze first appeared in Mesopotamia and Anatolia during the third millennium B.C., or Early Bronze Age (Pare 2000a:6–7). In the Mediterranean,the transition from arsenical to tin bronze took place during the course of the Middle Bronze Age (late third to early second millennium B.C.in the eastern Mediter-ranean, somewhat later in the west). The implication (Renfrew 1972:313–319) that tin bronze was an independent development in the northeast Aegean is contradicted by lead isotope analyses which show that most copper or bronze objects from sites such as Troy, Poliochni, and Kastri were not produced from local ores (Muhly and Pernicka 1992; Pernicka 1998:140–141). Exactly what caused the transition from arsenical to tin bronze is not well understood: as an alloy, tin bronze is not mechanically superior to arsenical copper (Pernicka 1998:135–136).Unlike arsenic, moreover, tin is not widely available as a mineral, and new trade networks would have been required to enable its distribution. However, it may have been easier to control the quality of tin bronze, and the production of tin bronze would have overcome the problem of working with toxic arsenic fumes (Charles 1978:30;Pare 2000a:7).

Given the limited number of tin deposits in the region, the source(s) of tin usedin the prehistoric eastern Mediterranean has always been a highly controversial issue. The suggestion that Afghanistan served as a prime source of tin for Bronze Age eastern Mediterranean societies is based in part on the existence of its rich tin resources (Muhly and Pernicka 1992:315;Weeks 1999:60–61).Muhly (1999:21) recently argued that Afghanistan or central Asia provided the tin that supplied the bronze industries of Mesopotamia, Anatolia, and the eastern Mediterranean, including Cyprus. Cuneiform documents from the early second millennium B.C., moreover, point to a trade network that brought tin from the east to the early states of Anatolia and Mesopotamia (Maddin et al.1977:41:Weeks 1999),and thence to the Mediterranean. Weisgerber and Cierny (2002,with fuller references) now maintain that prehistoric tin mining (second millennium B.C.), attested at the sites of Karnab (Uzbekhistan) and Musciston (Tajikistan), provided an important source of tin for Anatolia and Mesopotamia, if not for the Mediterranean. In contrast, Yener and Vandiver (1993) have argued that (very limited) tin deposits in the Taurus Mountains of southern Turkey were exploited during the Early Bronze Age. Their argument has been challenged by several scholars (e.g.,Muhly 1993;Weisgerberand Chierny 2002:180–181;papers in Journal of Mediterranean Archaeology 5[1995]) who maintain that the archaeological evidence is unclear,and far too limited to demonstrate anything beyond local use. Even if tin from the Taurus were mined during the Early Bronze Age, it now seems more likely that central Asia provided at least some of the tin used during the Middle-Late Bronze Ages,when tin bronze was far more widely produced, traded, and consumed in the Mediterranean. 

... 

By the Late Neolithic period (ca.4800–3100 B.C.), most people living in the Mediterranean region produced their own food, lived the year round in sedentary communities and increasingly were involved in intricate social and economic exchanges. By the beginning of the Bronze Age, certain alliances, special-interest groups, or even individual local leaders came to control access to raw materials in demand: obsidian, precious or semi-precious stones, metals such as gold, silver, copper, and tin, and a range of more perishable goods. From about 3000 B.C.onward – corresponding to the Chalcolithic period (Argaric culture) in Spain, the Final Neolithic in Italy, and the Early Bronze Age in the Aegean and eastern Mediterranean – the production and trade in metals increasingly became a key factor in promoting social change (Giardino 2000b;Knapp 1990a;Levy et al.2002;Manning 1994;Ruiz Taboada and Montero Ruiz 1999).  

...  

Technological innovations may be seen as progressive by managers and elites, but for the people who mined ores or smelted metals they were also potentially disruptive, forming the backdrop for social change as well as social abuse (Heskel andLamberg-Karlovsky 1980:260–261;Stollner 2003:427–429). Miners and metal-smiths often use ideology as a means to maintain, resist,or change their power base within society. Because elites who control and organize metallurgical produc-tion often use material culture to restructure relations of power (Gamble 1986:39), we may also expect such transformations to be visible in the archaeological record. 

...  

Consequently, there is little room to doubt that innovations in technology had deep-seated and long-lasting social and ecological effects, placing constraints as well as conferring benefits on Bronze Age mining and metallurgical production. In social terms, whereas the intensified production of copper employing an advanced technology did not preclude a strong sense of local community, such factors served to increase social distinctions between those at the top of the control structure and those at the bottom (Hardesty 1988:102,116;Knapp 1986b;2003). 

...  

The trade in metals during the Chalcolithic period was carried out on a very limited scale, and most metals were certainly consumed in the same area where they were produced (cf.Gale 1991). During the Early Bronze Age (third millennium B.C.), technological innovations like the longboat and sail facilitated the bulk transport of raw materials or manufactured goods on a much larger scale than ever before (Broodbank 1989). 

... 

Metals and metallurgy wielded an immense impact on Mediterranean Bronze Age societies, clearly evident in all the fundamental changes seen in the archaeological record from the end of the Chalcolithic period (Copper Age) onward. During the Bronze Age,innovations in maritime transport and the earliest cultivation of olives and vines stimulated the economy of the Mediterranean region and spurred some of its inhabitants to produce metals, take part in maritime trade, manufacture distinctive artifacts, and build domestic and public structures that represented the earliest towns and ceremonial complexes in the Mediterranean. The advent and spread of metallurgy promoted greater social distinctions,as certain individuals or groups acquired new wealth and prestige items. Because tin had to be imported in order to produce bronze, long-distance trade was stimulated. Duringthe second millennium B.C., gold, silver, copper, and tin came to represent what Sherratt (2000:83) has termed “convertible”value, both in an economic sense and in the literal sense that they could be consumed, stored, redistributed, or recycled in diverse forms and for various symbolic or ideological ends.Such documentary evidence as exists, exclusively in the eastern Mediterranean, is frequently preoccupied with these self-same metals (Liverani 1990:205–223,247–266;Moran,inKnapp 1996:21–25).

A remarkable series of social and economic changes thus were linked closely to all the innovative developments in extractive and metallurgical technologies,and tothe increasingly widespread and intensified production and distribution of metalsand metal objects. These changes include but are not limited to: (1) the proliferation of settlements and the emergence of town centers;(2) the development and expansion in interregional trade;(3) the growth of palatial regimes and city-state kingdoms,with their attendant writing systems (notably in the eastern Mediterranean);(4) the development and refinement of craft specialization and the spread of an iconographic koine;(5) the elaboration of mortuary rituals and burials with large quantities of precious metal goods;(6) the widespread occurrence of metal hoards and the related trade in recycled and scrap metal. The circulation of goods, ideas, and ideologies across geographic,cultural,and economic boundaries represents a social transaction,one that entangled producers, distributors, and consumers in wider relations of alliance and dependence, patronage and privilege, prestige and debt (Thomas 1991:123–124). Certain occupational identities came to be focused around metallurgical production and trade, and Cyprus even gave its name to the island’s most prominent product: copper ore (Muhly 1973:174–175).The coming of the Age of Iron, subsequent to all the developments discussed in this study, itself relied on extractive and smelting technologies developed during theBronze Age,together with the use of carburization, all of which are linked directly(albeit over the millennia) to the dramatic social and economic changes that ushered in the Industrial Revolution and the beginnings of the modern era.If it is indeed the case that “metals make the world go round” (Pare 2000b),nowhere can this slogan be better and more widely illustrated than in the prehistoric Bronze Age of the Mediterranean.

Archaeometallurgy in the Mediterranean: The Social Context of Mining, Technology, and Trade

Vasiliki Kassianidou and A.Bernard Knapp

Link

ORBIS: The Stanford Geospatial Network Model of the Roman World

A very useful new tool.

Screenshot:

Example output:


The fastest  journey from Roma to Constantinopolis in January takes 20.7 days, covering 2951 kilometers.
Prices in denarii, based on the use of a faster sail ship and a civilian river boat (where applicable), and on these road options:
 * Per kilogram of wheat (by donkey): 4.37
 * Per kilogram of wheat (by wagon): 4.99
 * Per passenger in a carriage: 580.42

Agriculture arrived in Cyprus 10,600 years ago

PNAS doi: 10.1073/pnas.1201693109

First wave of cultivators spread to Cyprus at least 10,600 y ago

Jean-Denis Vigne et al.

Early Neolithic sedentary villagers started cultivating wild cereals in the Near East 11,500 y ago [Pre-Pottery Neolithic A (PPNA)]. Recent discoveries indicated that Cyprus was frequented by Late PPNA people, but the earliest evidence until now for both the use of cereals and Neolithic villages on the island dates to 10,400 y ago. Here we present the recent archaeological excavation at Klimonas, which demonstrates that established villagers were living on Cyprus between 11,100 and 10,600 y ago. Villagers had stone artifacts and buildings (including a remarkable 10-m diameter communal building) that were similar to those found on Late PPNA sites on the mainland. Cereals were introduced from the Levant, and meat was obtained by hunting the only ungulate living on the island, a small indigenous Cypriot wild boar. Cats and small domestic dogs were brought from the mainland. This colonization suggests well-developed maritime capabilities by the PPNA period, but also that migration from the mainland may have occurred shortly after the beginning of agriculture.

Link

Genetic structure of North-East Sardinia (Pardo et al. 2012)

European Journal of Human Genetics , (29 February 2012) | doi:10.1038/ejhg.2012.22

Dissecting the genetic make-up of North-East Sardinia using a large set of haploid and autosomal markers

Luba M Pardo et al.

Abstract

Sardinia has been used for genetic studies because of its historical isolation, genetic homogeneity and increased prevalence of certain rare diseases. Controversy remains concerning the genetic substructure and the extent of genetic homogeneity, which has implications for the design of genome-wide association studies (GWAS). We revisited this issue by examining the genetic make-up of a sample from North-East Sardinia using a dense set of autosomal, Y chromosome and mitochondrial markers to assess the potential of the sample for GWAS and fine mapping studies. We genotyped individuals for 500K single-nucleotide polymorphisms, Y chromosome markers and sequenced the mitochondrial hypervariable (HVI–HVII) regions. We identified major haplogroups and compared these with other populations. We estimated linkage disequilibrium (LD) and haplotype diversity across autosomal markers, and compared these with other populations. Our results show that within Sardinia there is no major population substructure and thus it can be considered a genetically homogenous population. We did not find substantial differences in the extent of LD in Sardinians compared with other populations. However, we showed that at least 9% of genomic regions in Sardinians differed in LD structure, which is helpful for identifying functional variants using fine mapping. We concluded that Sardinia is a powerful setting for genetic studies including GWAS and other mapping approaches.

Link

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.

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."

Another look at Oetzi with 'euro7' and 'world9' calculators

After taking the first look at the genome of the Tyrolean Iceman, I decided to run him through a couple more calculators developed by the Dodecad Project.

The first one was euro7 which has a little bit more resolution within Europe. Oetzi was:

• 37.8% Southwestern
• 37.7% Southeastern
• 22.5% Northwestern
• 1.9% African
• 0.1% Far_Asian

These results are consistent with his K12b "Atlantic_Med" major ancestral component, and he appears once again to be a very close match for the Sardinian components using the same calculator.

The second one was world9 which is a "global" calculator that includes Amerindian and Australasian components. Oetzi was:

• 47.3% Atlantic_Baltic
• 46.4% Southern
• 3.1% Caucasus_Gedrosia
• 1.7% Australasian
• 0.9% African
• 0.6% East_Asian

Again, these match quite well the world9 values for Sardinians, who are a bit more Atlantic_Baltic and a little less Southern than Oetzi, as noted before for the K7b comparison that is similar to world9, with the addition of the Amerindian and Australasian components.

Overall, this is a nice demonstration that Oetzi's genome is indeed Sardinian-like as argued by Keller et al., and also that the Dodecad Project calculators based on the idea of "zombies" are indeed working as they're supposed to. (Note that the previous K=7 and K=12 comparisons were not based on "zombies", but produced quite the same conclusion as the supervised runs in this post).

This is even more impressive as only ~44k SNPs were used in these various experiments, intersecting the set of SNPs I have for Oetzi (1,459,228 SNPs mapped to hg18, or 156,691 SNPs intersected with my main Stanford HGDP reference), with the ~160-170k SNPs used in my various calculators after linkage disequilibrium-based pruning.

So, despite an about 4-fold reduction in the number of SNPs, the results are excellent. Hopefully, in the future, I'll find some time to create new calculators that use all ~160k of Oetzi's SNPs, although intersection with all the dozen Illumina-based datasets I currently have available leaves only ~72k SNPs in all.

But I have to say that I'm already growing tired of Oetzi, with his Sardinian-like predictability: what's the next ancient genome in the works? (e-mail me if you want to tip me)

Interpreting the Beaker phenomenon in Mediterranean France

Antiquity Volume: 86 Number: 331 Page: 131–143

Interpreting the Beaker phenomenon in Mediterranean France: an Iron Age analogy

Olivier Lemercier

The author offers a new descriptive explanation of the Beaker phenomenon, by focusing on Mediterranean France and making reference to the Greek influx in the same area 2000 years later. In the Iron Age, the influence began with an exploratory phase, and then went on to create new settlements and colonise new areas away from the coast. The Beaker analogy is striking, with phases of exploration and implantation and acculturation, but adjusted to include a final phase where Beaker practice was more independent. Comparing the numerous models put forward to explain it, the author shows that immigration and a cultural package are both aspects of the Beaker phenomenon.

Link

New study on Sardinian Y-chromosomes/mtDNA/Y chromosomes

Quite topical, given the recent publication of the genome of the Tyrolean Iceman and his unexpected relationship with present-day Sardinians.

European Journal of Human Genetics advance online publication 29 February 2012; doi: 10.1038/ejhg.2012.22

Dissecting the genetic make-up of North-East Sardinia using a large set of haploid and autosomal markers

Luba M Pardo et al.

Abstract

Sardinia has been used for genetic studies because of its historical isolation, genetic homogeneity and increased prevalence of certain rare diseases. Controversy remains concerning the genetic substructure and the extent of genetic homogeneity, which has implications for the design of genome-wide association studies (GWAS). We revisited this issue by examining the genetic make-up of a sample from North-East Sardinia using a dense set of autosomal, Y chromosome and mitochondrial markers to assess the potential of the sample for GWAS and fine mapping studies. We genotyped individuals for 500K single-nucleotide polymorphisms, Y chromosome markers and sequenced the mitochondrial hypervariable (HVI–HVII) regions. We identified major haplogroups and compared these with other populations. We estimated linkage disequilibrium (LD) and haplotype diversity across autosomal markers, and compared these with other populations. Our results show that within Sardinia there is no major population substructure and thus it can be considered a genetically homogenous population. We did not find substantial differences in the extent of LD in Sardinians compared with other populations. However, we showed that at least 9% of genomic regions in Sardinians differed in LD structure, which is helpful for identifying functional variants using fine mapping. We concluded that Sardinia is a powerful setting for genetic studies including GWAS and other mapping approaches.

Link

Complete genome of the Tyrolean Iceman

I'll update this post once I read the paper. I could not locate a source for the data after a quick scan of the paper, but:

After genotyping, we merged both HapMap and 1,000 Genomes genotypes with the Popres/Iceman-merged dataset, resulting in a final analysis dataset containing 125,729 SNPs. PCA was then performed on all samples, excluding the five 1,000 Genomes samples, which were subsequently projected onto the PC space inferred from the rest of the dataset.

UPDATE: The Iceman's genome can be found at the http://icemangenome.net site.

UPDATE I (Y-chromosome):


From the paper:

We addressed this issue here by analysing the G2a4-defining L91 SNP in 7,797 chromosomes from 30 regions across Europe. Fig. 3d shows the spatial frequency distribution of G2a4 throughout Europe. The highest frequencies (25 and 9%) occur in southern Corsica and northern Sardinia, respectively, (Fig. 3e) while in mainland Europe the frequencies do not reach 1%.

UPDATE II (Autosomal DNA): 

In terms of autosomal DNA, the Iceman clearly clusters with modern Sardinians, and also appears slightly more removed than them compared to continental Europeans. Interestingly, at least as far as the PC analyssi shows, Sardinians appear to be intermediate between the Iceman and SW Europeans, rather than Italians. Perhaps, this makes sense if the Paleo-Sardinian language is indeed related to languages of Iberia.

I don't see a downloadable version of the Iceman's genome at the icemangenome.net site, but I've asked the corresponding author for a PLINK/EIGENSOFT version of it. I anticipate that, as I've predicted, this will appear to be largely "Mediterranean" according to Dodecad v3, or "Atlantic_Med" according to the newer K12b calculator. It appears that there has indeed been Sardinian continuity against a backdrop of European discontinuity.

UPDATE III (Sardinians):


The Iceman's genome also places the Sardinian genetic isolate into new light. Two explanations have been proposed for the fact that Sardinians appear genetically distinctive vis a vis continental Europeans:

1. Sardinians have lost due to drift alleles that were present in continental Europe
2. Continental Europeans have gained alleles that were not present in their Sardinian-like ancestors

The Iceman's genome argues strongly in favor of the latter hypothesis: continental Europeans, or, at least North Italians c. 5,300 years ago were more Sardinian-like, and they have become less Sardinian-like up to the present, probably due to an influx of new populations, carrying new alleles. As more ancient DNA is recovered, we will slowly witness the transformation of gene pools over time.

Nature Communications 3, Article number: 698 doi:10.1038/ncomms1701

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

Andreas Keller et al.

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

Link