ISBA 2014 titles

Some interesting talks and posters from the upcoming International Symposium on Biomolecular Archaeology. I don't see any abstracts on the site (yet?) but the titles are intriguing. Some that caught my eye:

• Investigating the maternal lineage diversity from an early medieval site in Southern Italy
• Ancient mitochondrial and Y chromosomal DNA reveals the western Carpathian Basin as a corridor of the Neolithic expansion
• Ancient mitochondrial DNA from the Northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process
• The effect of demography and natural selection on pigmentation heterogeneity in late Pleistocene and early Holocene Europeans
• The genomics of equine speciation and domestication
• Ancient population genetics: new insights on horse domestication
• Species identification and analysis of the Tyrolean Iceman's clothes using next generation sequencing of ancient DNA.
• Early evidence for the use of pottery: extending the ancient lipid record to the Pleistocene.
• Whey to go – first identification of lactose in prehistoric pottery
• Use of the earliest pottery on the Western and Eastern side of the Baltic
• The geographical distribution of the Polynesian cultural complex and its association with P33-C2a1 Y chromosomes: adding data from Aotearoa (New Zealand)
• Interdisciplinary investigation of an archaic hominin femur from the Swabian Jura (South-West Germany)
• Tracing the genetic history of farming populations of El Portalón Cave in the Sierra de Atapuerca, Spain.
• Ancient human genomes suggest three ancestral populations for present-day Europeans
• Ancient DNA from Early Neolithic farmers in Europe
• Genomic diversity and admixture in Stone-Age farmer and hunter-gatherer groups in Scandinavia
• Ancient DNA reveals the complex genetic history of the New World Arctic
• A prediction of the hybridisation potential between Hominin species using mitochondrial DNA
• Population Genomics of Vikings
• Tracing the genetic profile of Sus scrofa on Romanian territory from the Neolithic period until the Middle Ages
• The origins of the Aegean palatial civilizations from a population genetic perspective
• Ancient DNA evidence for a diversified origin of ancestor of Han Chinese

European pigs replacing Near Eastern ones in Iron Age Israel

Related:

• The comings and goings of Near Eastern and European domestic pigs (Ottoni et al. 2012)

Scientific Reports 3, Article number: 3035 doi:10.1038/srep03035

Ancient DNA and Population Turnover in Southern Levantine Pigs- Signature of the Sea Peoples Migration?

Meirav Meiri et al.

Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution.

Link

EAA 2013 abstracts

The bioarchaeology of the neolithic Carpathian Basin

By the beginning of the 6th Millennium cal BC, the first farmers reached the Carpathian Basinwhere the last transition to food production and sedentary life took place. The early neolithic groups became restructured both in their cultural and genetic composition in the 6th and 5th Millennium BC, affected by at least five major Northern Balkan impulses. The western part of the area became a major communication zone, mediating between South Eastern and Central Europe. Our working group has been focusing on this early population history of Eastern Hungary and of Transdanubia, developing and comparing ancient DNA, stable isotope, osteological and archaeological data gained from not less than 600 neolithic skeletons (6000–4300 cal BC).  

In the session we would like to give an account of the DNA and stable isotope (SR, N, C) analysis, carried out within the frames of a three-year interdisciplinary project funded by the German Research Foundation along with the co-evaluation of these results with osteology and zooarchaeology, as well as giving a comparative interpretation of this data within our present socioarchaeological knowledge.

The megalithic past of the Bronze Age kurgans of the North Pontic Region 

The Early Bronze Age (EBA) burial mounds (kurgans) in the western part of the North Pontic Region (NPR) display a tendency to be erected over earlier megalithic ritual constructions. The initial purpose of these megalithic structures might have been cosmology-related. In succeeding time periods the initial astronomic purpose could have been forgotten and these megalithic sites became designated at sacred places suited for distinguished burials. Megalithic elements comprising the initial constructions became incorporated into the subsequent burials. The Revova kurgan from western NPR is one such construction. It was erected over a megalithic structure in a shape of a tortoise with the stone elements of the construction being astronomically aligned. An assembly of disarticulated human remains deposited in the center of the construction dated to the Eneolithic (4200 BC). On the other hand, the layout of stones comprising the “Tortoise” appears to most accurately line up with the movement of celestial objects as they appeared on the sky around 6300 BC. Mitochondrial DNA lineage extracted from the remains was characteristic to the Mesolithic/Neolithic hunter-gatherer populations from northern Europe as well as Bronze Age groups from south Siberia. 

The spread of domestic pig in the central and Eastern part of the Romanian territory described by the ancient mithochondrial DNA

Previous genetic analysis showed the presence of two different haplotypes for domestic pigs from 11 different sites in the South-Eastern part of Romania: the Near-Eastern haplotype ANC-Y1-5A, for 18 individuals, and ANC-Aside european haplotype, for 8 individuals. This study reveals the genetic signature for other 52 samples (5000–3500 BC, from 7 archaeologic sites) covering the central and Eastern parts of Romania. After the DNA extraction, PCR, and sequencing, no ANC-Aside haplotype was found, but, apart from the Near-Eastern ANC-Y1-5A haplotype, identified in the majority of domestic pig samples, the european ANC-Cside haplotype (generally identified in the wild boars), was also found in three domestic pigs from Poduri, Ghigoiesti and Trusesti. The wide spread of the wild boar with the ANC-Cside haplotype not only on the entire Romanian territory, but also, as previously shown, in it’s close proximity, and the emergence of this genetic signature in both wild and domestic pigs from three different sites could support the idea of a local domestication of the wild boar after 4500 BC, in this specific area.

The genetic make-up of the Linear Pottery culture

The Linear Pottery culture (LBK) is one of the first Central European Neolithic farming cultures marking the transition from a hunter-gatherer to a farming lifestyle. The LBK is thought to have originated from Early Neolithic cultures in the Carpathian Basin from where it extended across Europe over a vast distribution area spanning from the River Rhine to the Ukraine. Consequently, its role during the process of Neolithisation in Central Europe is subject of a long-standing debate in archaeology, anthropology and human genetics. Ancient DNA studies have provided direct insights into Mesolithic and Neolithic mitochondrial diversity indicating genetic discontinuity between Central Europe’s autochthonous hunter-gatherers and LBK populations. Comprehensive population genetic analyses utilizing large databases of present-day populations have disclosed genetic affinities of the LBK to the modern-day Near East, Anatolia and the Caucasus, supporting genetic influx from this region into Central Europe at the advent of farming and explaining the apparent genetic discontinuity between foragers and farmers. We will summarize the inferences that have been drawn from 108 LBK data to provide an overview of genetic diversity of the first farming communities in Central Europe, which represents an invaluable genetic perspective for the discussion of the Neolithic in the Carpathian Basin.

Bell Beaker child burials and their gender identity in the light of DNA analysis

The DNA analysis of 53 child burials from the Bell Beaker cemetery at Hostice-I produced data on 21 sexed individuals. Out of 14 burials with male gender attributes were 12 individuals biologically male and two determinate as women. Cases of girls that were brought up as boys probably existed in 3rd Millennium BC burial customs. Out of seven children buried in the female position only 1 was actually biological female (juvenile 15–20 years) and 6 male (2 juvenile 15–19/20 years). That means four boys (aged 3–4, 7, 8–12, 15) were in fact buried as women. Such a result is in line with known demographic unbalance within Beaker cemeteries. Most young girls were not buried at the communal cemetery and considerable number of boys were buried in the female fashion. This is rather high number of cases when the masculine attributes were downplayed in the burial customs and it is hard to interpret whether they were boys supposed to be brought up as women or they had yet no right to act as men, unlike some other sub-adult boys, perhaps members of families with ascribed hereditary warrior status. It almost seems that some young boys were socially considered to be girls, perhaps until ceremonial rite of passage, social initiation of some kind.

Ancient Human DNA – A problem of interpretation

The problem with ancient human DNA is not contamination with modern human DNA any more. This still happens, but aDNA scientists can now recognise it and deal with it. The problem is with the overinterpretation of results. Only a few mitochondrial and Y chromosome aDNA sequences may be obtained from a burial assemblage, but these are interpreted in a population genetics framework which incorporates DNA sequences obtained from present day populations. This type of analysis ignores the possibility that social structures can affect genetic outcomes, as is seen in traditional societies and has recently been recognised by evolutionary geneticists. Societies practising patrilocal exogamy versus endogamy have been studied and the mtDNA and Y chromosomal haplotype diversity analysed. Patrilocal societies show high mtDNA diversity while Y haplotype diversity is reduced. Endogamous societies do not show the reduction in Y diversity, but mtDNA diversity is maintained. Ancient DNA results from several Neolithic sites can therefore be interpreted to identify the type of social structure present. Patrilocal exogamy is the most parsimonious interpretation and this is corroborated by Sr isotope studies from LBK sites.

 Ancient DNA discloses multiple migrations into Central Europe during the Neolithic

The Central European Neolithic is characterised by a succession of differentiated archaeological cultures indicating a period of fundamental cultural change. A recurrent question in archaeology and anthropology is whether cultural change in prehistory was accompanied by variation in the gene pool of associated populations. Ancient DNA studies based on mitochondrial DNA revealed a discontinuity between Central Europe’s autochthonous hunter-gatherers and their early farmers and between the latter and the present-day population, suggesting further migration events after the initial Neolithisation. However, to date little attention has been drawn to cultural and potentially population changes in subsequent Neolithic periods. To investigate this issue, we conducted a large chronological study including a succession of nine cultures from the Mittelelbe-Saale region, Saxony-Anhalt, Germany to reconstruct a detailed temporal profile of cultural and genetic diversity in Central Europe. The presented diachronic study spans overall 3,950 years from the beginning of the Neolithic period and the introduction of producing subsistence strategies ~5,500 BC to the appearance of structured chiefdoms in the Early Bronze Age ~2,200–1,550 BC. This transect through time identified multiple population dynamic events during the Neolithic, which involved genetic influx from various regions in Europe.

 Ancient DNA and isotope analysis of the Starčevo graves at Alsónyék-Bátaszék

Between 2006 and 2009 at Alsónyék-Bátaszék a settlement with 26 graves of the Starčevo culture were unearthed. More than 400 various features belonged to this early Neolithic period on an extension of 80 hectares. The archaeological findings underline the significance of Alsónyék-Bátaszék, which is to date the largest Starčevo site uncovered in present-day Hungary. We analysed the 26 Starčevo burials from Alsónyék from ancient DNA and stable isotopic aspects, involving them in our three-year bioarchaeological Neolithic project. The excellent DNA preservation made it possible to gain reproduced mitochondrial DNA results from all skeletons, and we could additionally type the Y chromosome in 5 of the male individuals. The strontium (87Sr/86Sr) and oxygen (δ18Op) isotopic data obtained an insight into the mobility and kinship system of the population. The carbon (δ13C) and nitrogen (δ15N) isotope analyses of the skeletons supported a basis for a diet reconstruction, supplementing the archaeozoological proceedings of the site. Our results from the Alsónyék-Bátaszék Starčevo specimens, dated between ca. 5800-5500 cal BC, denote a milestone of the early Neolithic bioarchaeological studies in Transdanubia.

 6–5th millennium BC cultural changes in Western Hungary tested by ancient DNA

Western Hungary (Transdanubia) was one of the key regions at the process of Neolithisation in Central Europe. The Starcevo culture, representing the earliest farmers on this region, settled down at latest 5750 cal BC south of the Lake Balaton. It had a major role in the formation of the Linearbandkeramik culture in Transdanubia. The following Sopot, Lengyel cultures of the late Neolithic and Early Copper Age Transdanubia show repeated cultural influences from the Balkan, besides local extant cultural traditions. 

The focus of our study is the process of these cultural changes in Transdanubia, in the view of ancient DNA, investigating mitochondrial and Y chromosomal lineages and markers. A total of 292 skeletons were sampled and processed, with an overall success rate of 89% for mitochondrial DNA. Comparing the mitochondrial and Y chromosomal results with other published data and evaluating them with population genetic analyses, we gained a peerless insight into the population history of Western Hungary. 

Our study may give an additional help to prehistoric archaeology, for a better understanding of the nature of cultural changes, supporting it with a new type of evidence, in order to see Transdanubia as a mediating area between South East and Central Europe.

European hunter-gatherers acquired pigs with Near Eastern and European mtDNA

This is a nice demonstration of transfer of domesticated animals from Neolithic farmers to European hunter-gatherers. (Red=European, Yellow=Near Eastern).

Related: Ottoni et al. (2012).

Nature Communications 4, Article number: 2348 doi:10.1038/ncomms3348

Use of domesticated pigs by Mesolithic hunter-gatherers in northwestern Europe

Ben Krause-Kyora et al.

Mesolithic populations throughout Europe used diverse resource exploitation strategies that focused heavily on collecting and hunting wild prey. Between 5500 and 4200 cal BC, agriculturalists migrated into northwestern Europe bringing a suite of Neolithic technologies including domesticated animals. Here we investigate to what extent Mesolithic Ertebølle communities in northern Germany had access to domestic pigs, possibly through contact with neighbouring Neolithic agricultural groups. We employ a multidisciplinary approach, applying sequencing of ancient mitochondrial and nuclear DNA (coat colour-coding gene MC1R) as well as traditional and geometric morphometric (molar size and shape) analyses in Sus specimens from 17 Neolithic and Ertebølle sites. Our data from 63 ancient pig specimens show that Ertebølle hunter-gatherers acquired domestic pigs of varying size and coat colour that had both Near Eastern and European mitochondrial DNA ancestry. Our results also reveal that domestic pigs were present in the region ~500 years earlier than previously demonstrated.

Link

Local Origin of Domestic Pigs in the Upstream Region of the Yangtze River (Jin et al. 2012)

PLoS ONE 7(12): e51649. doi:10.1371/journal.pone.0051649

Mitochondrial DNA Evidence Indicates the Local Origin of Domestic Pigs in the Upstream Region of the Yangtze River

Long Jin et al.

Previous studies have indicated two main domestic pig dispersal routes in East Asia: one is from the Mekong region, through the upstream region of the Yangtze River (URYZ) to the middle and upstream regions of the Yellow River, the other is from the middle and downstream regions of the Yangtze River to the downstream region of the Yellow River, and then to northeast China. The URYZ was regarded as a passageway of the former dispersal route; however, this assumption remains to be further investigated. We therefore analyzed the hypervariable segements of mitochondrial DNA from 513 individual pigs mainly from Sichuan and the Tibet highlands and 1,394 publicly available sequences from domestic pigs and wild boars across Asia. From the phylogenetic tree, most of the samples fell into a mixed group that was difficult to distinguish by breed or geography. The total network analysis showed that the URYZ pigs possessed a dominant position in haplogroup A and domestic pigs shared the same core haplotype with the local wild boars, suggesting that pigs in group A were most likely derived from the URYZ pool. In addition, a region-wise network analysis determined that URYZ contains 42 haplotypes of which 22 are unique indicating the high diversity in this region. In conclusion, our findings confirmed that pigs from the URYZ were domesticated in situ.

Link

The comings and goings of Near Eastern and European domestic pigs (Ottoni et al. 2012)

This is an excellent paper whose findings re: pig domestication seem to parallel many of my own observations regarding the flow of human populations. It is open access, so you can read it for yourselves, but the following figure illustrates the situation admirably:

The left-right arrangement of the columns corresponds to a west-east longitude across West Asia. It can be easily seen that some of the early domestic samples (yellow, bottom row) are concentrated in the west (Y1 haplotype), while others (blue, Arm1T) in the east.

Neolithic European samples possessed the Y1 haplotype, but lacked the Arm1T one. So, the authors conclude that:

The ancient Anatolian data presented here reveal that both wild and possibly domestic Neolithic pigs (identified using traditional metrics) possessed Y1 haplotypes ... The presence of these lineages corroborates the supposition that the earliest domestic pigs in Europe originated from populations originally domesticated in the Near East, conclusively linking the Neolithization of Europe with Neolithic cultures of western Anatolia (Larson et al. 2007a; Haak et al. 2010).

I have repeatedly highlighted the "puzzle" of the early European Neolithic: the signature Y-haplogroup G2a was unaccompanied by other common Near Eastern lineages, and the modal "West Asian" ancestral component in present-day West Asian populations seems to have been absent in early Neolithic samples, which were dominated by a "Sardinian-like" population. I have argued that this meant that the European Neolithic was drawn from a limited founder source that was more "Mediterranean/Southern" autosomally than "West Asian", at least in terms of the components identified by the Dodecad Project.

In Europe itself, the early Near Eastern domestic pigs were replaced by European ones:

Ancient DNA extracted from early Neolithic domestic pigs in Europe resolved this paradox by demonstrating that early domestic pigs in the Balkans and central Europe shared haplotypes with modern Near Eastern wild boar (Larson et al. 2007a). The absence of Near Eastern haplotypes in pre-Neolithic European wild boar suggested that early domestic pigs in Europe must have been introduced from the Near East by the mid 6th millennium BC before spreading to the Paris basin by the early 4th millennium BC (Larson et al. 2007a). 

By 3,900 BC, however, virtually all domestic pigs in Europe possessed haplotypes  from an indigenous European domestication process (Larson et al. 2007a) only found in European wild boar. This genetic turnover may have resulted from the accumulated introgression of local female wild boar into imported domestic stocks, or from an indigenous European domestication process (Larson et al. 2007a).

We have seen that early Neolithic domestic pigs came from Western Anatolia, but apparently these did not last, but were replaced in Europe by pigs carrying mtDNA of European wild boar. An additional possibility is that the European wild boar were better adapted to local conditions in Europe, so the stock of European farmers gradually became "local" due to artificial/natural selection favoring the local "European" type. It might also be that in accordance with Bergmann's rule, European-descended pigs were simply bigger, and thus more economically productive.

In any case, the interesting thing is that pigs carrying the "European" haplotype went the other way, crossing from Europe to Asia. The beginning of this process seems to have occurred in the Middle Bronze Age:

The temporal and geographic distribution of genetic haplotypes presented in our study demonstrates that the first AMS dated pig with European ancestry (haplotype A) appeared almost 1,000 years earlier than the Armenian samples in a Late Bronze Age context (~1,600-1,440 BC) at Lidar Höyük (fig. 1). An even earlier Middle Bronze Age specimen from the same site also possessed a European signature, but a direct
AMS date for this specimen could not be obtained.

I have written how increased mobility and long-range networks associated with the new metallurgical class facilitated commerce during the Bronze Age. The authors suggest the possibility of Minoan-Mycenaean/Hittite involvement during the Bronze Age, which are certainly plausible conduits for European pigs to have crossed the Aegean at this time. But, as you can see from the figure, the "European" pigs are still outliers during the Middle and Bronze Ages, but become common in the Iron Age sample from Lidar Höyük, and eventually replacing local types throughout Anatolia and Armenia, but, apparently, not Iran:

The frequency of pigs with European ancestry increased rapidly from the 12th century BC, and by the 5th century AD domestic pigs exhibiting a Near Eastern genetic signature had all but disappeared across Anatolia and the southern Caucasus. Though we did not detect European signatures in the ancient Iranian samples (fig. 1), the eastward spread of European lineages may have continued into Iran later than the Iron Age since European lineages have been found in wild caught modern Iranian samples (Larson et al. 2007a).

Of course a 12th century BC increase in European domestic pigs is entirely consistent -chronologically- with the Phrygian/Armenian settlement in Anatolia, and this association is further reinforced by the lack of European signatures in pigs from Iran where Phrygo-Armenians did not settle. The increase in European pigs could later be mediated by the Greek colonization, and the increase in trade during antiquity, just as trade would later introduce East Asian pig DNA into Europe.

The beautiful temporal transect presented in the Figure may also prove useful for students of ancient human DNA. I'd love to see how humans living close to sites #14-16, dominated by Arm1T haplotypes throughout history might differ from those of Neolithic West Anatolia, and whether the "mixed" Iron Age sample from Lidar Höyük shows evidence of the arrival of European-like human populations to accompany the European pigs.

Mol Biol Evol (2012) doi: 10.1093/molbev/mss261

Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics

Claudio Ottoni et al.

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or appeared so as a result of admixture between introduced pigs and European wild boar. These pigs not only replaced those with Near Eastern signatures in Europe, they subsequently also replaced indigenous domestic pigs in the Near East. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria and Turkey. Our results firstly reveal the genetic signature of early domestic pigs in Eastern Turkey. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, nearly 1,000 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the demographic and societal changes during the Anatolian Bronze and Iron Ages.

Link

Pig genome + admixture into European wild boars

Of interest: 

The domestic pig (Sus scrofa) is a eutherian mammal and a member of the Cetartiodactyla order, a clade distinct from rodent and primates, that last shared a common ancestor with humans between 79 and 97 million years (Myr) ago1,2 (http://www.timetree.net). Molecular genetic evidence indicates that Sus scrofa emerged in South East Asia during the climatic fluctuations of the early Pliocene 5.3–3.5 Myr ago. Then, beginning ~10,000 years ago, pigs were domesticated in multiple locations across Eurasia3 (Frantz, L. A. F. et al., manuscript submitted).

also:

We found a clear signal for admixture between North Chinese and European populations of wild boars that we interpret as migrations across Eurasia during the later stage of the Pleistocene (Supplementary Table 24). Moreover, this hypothesis is further supported by the high value of concordance factor on the X chromosomes (Supplementary Table 20). The demographic analysis shows that the last glacial maximum (LGM)-induced bottleneck had similar magnitude in Europe and North China (Figure 2, main text). Together, these evidences suggest the existence of another (besides Asian + European) biogeographic zone for pigs, extending across North Eurasia. 

... 

There was a strong signal for admixture from Asian into European breeds. We found that European domestic breeds such as Landrace and Large White have a significant amount of Asian genetic material (Supplementary Table 24). This admixture is likely to be due to importation of Chinese breeds into Europe (especially UK) at the onset of the 'agricultural' revolution in the late 18th and 19th century.

Nature 491, 393–398 (15 November 2012) doi:10.1038/nature11622

Analyses of pig genomes provide insight into porcine demography and evolution

Martien A. M. Groenen et al.

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Link

Before Silk: Unsolved Mysteries of the Silk Road by Colin Renfrew

A great talk by Colin Renfrew at the Penn Museum, a must view for anyone interested in Eurasian prehistory. It's good to know that Renfrew holds that the Tocharians originated in West Asia and spread along the Silk Road (south of the Caspian) and not along the steppes. That is also my opinion, and I would perhaps associate them with the J2a/R1b-rich population of eastern Anatolia, Trascaucasia and North Iran, and, perhaps, even related to the Gutians from the Zagros (after Gamkrelidze and Ivanov). That would explain quite well, I believe the anomaly that is the high J2a/R1b frequency in the region.

Also, I would disagree with long-term persistence of Tocharian in Xingiang; it's more likely that this was due to a late migration from somewhere to the west that was eventually swamped by the much more successful wave of the Indo-Iranians that must've involved a J2a/G2a/R1a1 combination. I've made the point before that the vast majority of the territory of Europe and West Asia has shifted language (if not language family) over a span of 2-3 thousand years, so I see no real reason to imagine 2-3 thousand years of linguistic continuity in Xinjiang until the 8th c. AD when Tocharian is first attested.

UPDATE:

Here are various abstracts from the Symposium Reconfiguring the Silk Road: New Research on East-West Exchange in Antiquity; hopefully more videos will be uploaded.

UPDATE II:

James Mallory's talk is also uploaded:



He spends a great deal of his time establishing the (not controversial) idea that Tripolye cultures cannot explain the Yamna phenomenon east of the Dnieper. I will not argue with this, but it is rather a defensive stance of arguing against the spread of Indo-Europeans from the Balkans to the steppe-lands. Positive evidence for the spread of Yamna in the opposite direction is what is needed for the steppe model, and that is what is lacking: with the exception of some clearly Yamna-derived sites in the northern Balkans and Hungary, the links to the rest of the European Indo-Europeans are weak to non-existent.

Moreover, I would argue that the assumption that 3-4,000 years BC there were Indo-European speakers east of the Dnieper is itself suspect. There is no great necessity of explaining how Yamna was Indo-Europeanized from the Balkans, because there is no evidence that it was Indo-European. The first clearly attested Indo-European groups in the European steppe are the Scythians, and they appear in the 1st millennium BC, with both craniology and ancient sources agreeing that they were of eastern origin. So, the inability of the Balkan Tripolye Indo-Europeans of Indo-Europeanizing the Pontic steppe east of the Dnieper is really a non-sequitur, since one must first demonstrate that populations east of the Dnieper spoke Indo-European languages 3,000 years before a single branch of IE (the Iranic) appears in the region from the east.

Mallory also highlights some other substantial problems of the steppe model. Tocharian has IE words for cereals and pigs, and the evidence such as it is suggests that east of the Dnieper there were no domesticated cereals and no evidence of pigs. All this, of course, disappears once we accept that the Tocharians did not move across the steppe lands north of the Caspian, but south of it, from Iran and ultimately the Near East.

Mallory also points out that while he suspects Afanasievo to be linked to the Proto-Tocharians, the sum total of the evidence linking Xinjiang with Afanasievo is meagre. I would also add that, as I've explained above, if one were to establish links between Bronze Age Tarim and Afanasievo, that still leaves a couple of millennia until the first attestation of the Tocharian languages.

Another point of interest is the claim that Indo-Iranians and Tocharians must've been separated in space and time to evolve into so distinctive languages. But, that too is a non-sequitur. We only have to look at the Near East or the Caucasus to witness the co-existence of a handful of language families and dozens of distinct languages. You don't need a large separation to create a new language subfamily, but only a few rivers or high mountains, and Transcaucasia provides both in abundance. I would see Tocharians as the last remnant of the eastern Indo-Europeans, perhaps refugees from further west into Xinjiang itself, with Indo-Iranians pushing them eastward. As for the later steppe cultures that were unquestionably Iranic, these were probably formed after the collapse of the BMAC which sent off Indo-Aryan offshoots south in the 2nd millennium BC, and Iranic ones north, east, and west soon thereafter.

ISBA4 abstracts

Here are some interesting abstracts from the recent 4th International Symposium on Biomolecular Archaeology.

Naglaa Abu-Mandil1 & Terry Brown

Kinship analysis and sex identification of skeletons from two archaeological sites in Greece

Ancient DNA offers unprecedented opportunities for anthropologists and bioarchaeologists to assess the biological relationships of ancient populations. This study is designed to assess the family relationship among skeletons from two different archaeological sites in Greece which can help in shedding light on the ritual practice in Aegean prehistory. Another aim is to identify the sex of these skeletons genetically to confirm the conventional sexing methods. These sites are called Kouphovouno and Bostani. Kouphovouno is an important Neolithic and Bronze Age archaeological site near Sparta in Lakonia, while Bostani is dated back to the Early Helladic period in Ancient Greek history. In both cases the sites are recently excavated and DNA samples from all people who have handled the skeletons are available. Both mtDNA and nuclear DNA markers are being studied in order to identify maternal relationships and to reveal the sex of the skeletons.

Morten Rasmussen et al.
The nuclear genome of an ancient human

We have sequenced the complete genome from an ancient human. It was obtained from 4,000-year-old permafrost-preserved hair; the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20, we recover 79% of the diploid genome, and identify 353,151 highconfidence single-nucleotide polymorphisms (SNPs). Comparisons with SNP data from contemporary populations allow us to explore the migrations and kinship of this extinct culture. Analyses provide evidence of a migration from Siberia into the New World, independent of that giving rise to the modern Native Americans and Inuit. The migration was dated to approximately 5,500 years BP and the closest living relatives are found in North-East Siberia showing no signs of admixture with modern Native Americans or Inuit. We use functional SNP assessment to assign possible phenotypic characteristics of the individual.

This is extremely exciting as it speaks of Y-chromosome results from Central European Neolithic sites, which is a first. It seems to me that migrationism is due for a big comeback. If anyone has attended the symposium and/or has more information on this feel free to leave a comment/send me an e-mail.

Wolfgang Haak et al.
Ancient DNA from Early Neolithic Farmers suggests a major genetic input from the Near East

The Neolithic transition (approx. 8000-4000 BC) is considered one of the most important demographic events in Europe’s past since the initial peopling of anatomically modern humans in the Upper Paleolithic (40,000 BC). Whether this transition has been cultural or driven by large-scale population movements is subject of a long-standing scientific debate in archaeology, anthropology and human population genetics. So far, inferences about the genetic make-up of past populations have been drawn from studies of modern-day Eurasian populations, but ancient DNA studies now provide direct snapshots of specific time frames in the past.

We present new mitochondrial and Y-chromosomal data from Neolithic individualsfrom a Central European early farming site, Derenburg (Germany), which significantly extends the genetic dataset of the Linearbandkeramik (LBK; n=42), and provides the first detailed genetic picture of the earliest Neolithic culture in Central Europe (5500-5000 cal BC). Comprehensive population-genetic analyses utilizing a large database of modern-day Western Eurasian populations (n=23,394) reveal unique genetic features of the LBK population and a clearly distinct mitochondrial haplogroup frequency distribution. Importantly however, the LBK population shows an affinity to populations in the modern-day Near East, suggesting a major genetic input from this region at the time of the advent of farming in Europe.

I wish we knew what the haplogroups of the unambiguously defined samples were...

Silja Dillenberger et al.
Parallel tagged amplicon sequencing of highly degraded Ychromosomal DNA from archaeological skeletons

The intent of the study was to develop a Y-SNP multiplex-PCR suitable for genetic analysis of ancient human remains. Therefore 37 SNPs characterizing Eurasian
haplogroups, with a focus on Europe and Central Asia, were selected in order to get a
high phylogeographic resolution. The 37 SNPs, using amplicon lengths between 64 and 107bp, were co-amplified within 2 multiplex PCRs followed by parallel tagged sequencing on the 454 platform. After testing on 3 recent male and 2 recent female individuals it was applied to 8 male prehistoric samples from Central Asia and Europe. One sample was too poorly preserved for haplogroup identification. Another individual could be narrowed down to Q or R*. The haplogroups of the remaining 6 samples could unambiguously be defined. This shows that this approach is adequate for Y-chromosomal typing of highly degraded ancient human remains.

Five years ago I estimated an 11% contribution of Central Asian Turks to modern Anatolians, which seems quite inline with the following estimate. I will simply note that the number of 1.5 million is probably inflated, as the invaders did not have the same reproductive success as the local population; this means that the "original Turks" were fewer than 11%. Moreover, not all of the Anatolian population of the 11th century became present-day Anatolians; the current Muslims of Anatolia are a part of the 11th century population mixed with the invaders, and hence the number of invaders must've been even smaller.

Inci Togan et al.
An Anatolian Trilogy: Arrival of nomadic Turks with their sheep and shepherd dogs

Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, pastoral nomadic group from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. Central Asian genetic contribution to Anatolia with respect to the Balkans was estimated as 13% by an admixture analysis implemented in LEA. This estimate was obtained by employing nuclear genetic markers. MtDNA and Y-chromosome estimates confirmed this admixture proportion. Based on the population size estimation for Anatolia in 12th century, it can be calculated that at least 1.5 million nomads might have arrived to Anatolia. History tells us that they have arrived to Central and Eastern Anatolia first and only 150 years later they invaded Western Anatolia. Distributions of genetic diversity of domestic sheep and shepherd dogs in Turkey support that as well the language spoken in Anatolia these nomads have changed the genetic landscape of these two domestic species within Turkey. These observations have implications on conservation strategies of domestic sheep in Anatolia which is known to be the cradle of sheep domestication. Results must be confirmed by ancient DNA studies.

Alicia K Wilbur et al.
Ancient tuberculosis before and after the Age of Exploration

The Age of Exploration resulted in contact between human populations that were previously isolated from each other, initiating exchange of ideas, cultigens, and diseases. The modern biogeography of tuberculosis (TB) strains appears to reflect this with, for example, the presence of European type strains in the Americas and elsewhere. Until recently, it was thought that TB originated in the Old World in the last 10,000 years and the presence of TB in the Americas prior to contact was debated. Current estimates of TB’s origins, however, range from 3-6 million years ago. In our research, we attempt to characterize ancient mycobacterial strains from cases of disseminated bone TB in order to understand the phylogenetic relationships between strains of tuberculosis prior to and after the Age of Exploration. DNA was extracted from over 115 samples exhibiting classic tuberculosis lesions obtained from both the New and Old Worlds and ranging in age from 5800 BCE to A.D. 1800. Then, four quantitative PCR assays were used to gauge the preservation of host and pathogen DNA. Human nuclear and mitochondrial, and mycobacterial repetitive (IS6110) and single copy (rpoB) loci were analyzed. These results show that while approximately one third of the samples contain human nuclear and/or mitochondrial DNA, only 10% were positive for mycobacterial DNA. Mycobacterial DNA was usually recovered in the presence of human DNA (75%). In addition, our results suggest that TB strains in the Americas dating prior to European contact did not contain the IS6110 repeat element. From the samples that tested positive for host and mycobacterial DNA, we first selected two from Peru and one from Canada, for subsequent analyses using highthroughput pyrosequencing. Our analyses indicate that both slow-growing (pathogenic) and fast-growing (environmental) species of mycobacteria are present in the samples. However, our analyses also indicate that new methods for targeting specific sequences of interest are necessary to obtain sufficient genome coverage for evolutionary analyses. We will discuss ways of doing this and our current progress in this effort.

The New Scientist reports that the following study discovered a couple of Africans were present in the crew of Columbus.

Vera Tiesler et al.
Age at death, biological ancestry and provenience of Christopher Columbus’ crew at La Isabela, Santo Domingo, (1493-1498). Histological and biomolecular approaches

The site of La Isabela, in the Dominican Republic, was the first colonial town in the Americas. It was settled by Christopher Columbus and his crew at the beginning of AD 1494, and initially housed some 1,500 individuals from a wide array of social, economic and probably ethnic backgrounds. Its graveyard quickly accumulated the mortal remains of those who succumbed to the harsh conditions of the Atlantic crossing and life in the colony. In this study we present the preliminary results of a series of histological and molecular (isotopic and DNA) studies that expand on the macroscopic skeletal information in combination with detailed historical records on the lives of the deceased. Considered jointly, the data sets provide deepened insights into age at death, disease, nutrition, biological ancestry and geographic origins of 49 individuals unearthed between 1983 and 1991 and currently stored at the Museo del Hombre Dominicano in Santo Domingo, Dominican Republic. The analyses were largely funded by the Universidad Autónoma de Yucatan, Merida, Mexico, and National Geographic Society, Washington D.C., US, and received logistical support form the Museo del Hombre Dominicano, Dominican Republic.

Tracey Pierre et al.
American Southwest prehistory through ancient DNA

The American Southwest is one of the best archaeologically known areas of the world. It is also one of the most ethnically and linguistically diverse regions inhabited by contemporary Native American groups in North America. To what extent are the early and late prehistoric Southwest occupants associated with the Mesa Verde, Chaco Canyon, Mimbres and Basketmaker cultures related to today’s Athapaskan, Puebloan and Uto-Aztecan speakers? Is there genetic evidence for an earlier migration into the Southwest by populations ancestral to today’s Southern Athapaskans? Can the spread of farming into the Southwest region by Uto-Aztecan speakers from Mexico be detected in the gene pools of these earlier cultures? How are the former occupants of Chaco Canyon related to other prehistoric and modern inhabitants of this region? Does the current regional diversity reflect the geographical distribution of Southwest cultures prior to European contact? Previous ancient DNA research from the greater Southwest has demonstrated both regional continuity and discontinuity through the study of short-read mtDNA sequences. With the advent of second generation sequencing technology it is now possible to address in finer resolution these microcontinental migrations questions associated with the spread of language families into the American Southwest.

I don't want to comment too much on the following abstract, but I'm always favorably inclined to the prosaic rather than the ornate interpretations of ancient artifacts, unless there is clear evidence to the contrary.

Lucija Šoberl et al.
On the Beaker trail: Investigating the function of British Beakers through organic residue analysis

Beaker pottery is traditionally regarded as a material symbol of social, material and ideological changes that began in the latest Neolithic – these included the appearance of new ceramic technologies, modes of dress and adornment, the introduction of metallurgy and single burial. As far as the pottery goes, meticulous and numerous typological schemes have been produced in the past, but the function of Beakers has never been established on a larger scale from a scientific point of view.

British Beakers are most commonly found with inhumation burials, laid in pits or cists, and often in association with other objects. It has often been supposed that Beakers were produced specifically for grave deposition, since they differ in terms of fabric quality and decoration from those produced for non-funerary use. Due to their elaborate decoration and innovative fine fabric, Beakers have been considered as prestige items. As a consequence of Sherratt’s interpretation of Beakers as drinking cups, used to consume alcoholic beverages or narcotic substances at ritual gatherings, these vessels have gained almost a legendary status as prestige drinking equipment that has not been scientifically contested. The porous fabric of prehistoric pottery has been known to represent a favourable environment for the long term preservation of organic molecules, such as lipids. Beaker potsherds from funerary and non-funerary contexts have been analysed using solvent extraction, followed by gas chromatography, mass spectrometry and isotope ratio mass spectrometry to provide structure identification, biomolecular fingerprints and compound specific δ13C values.

Through analyses of absorbed lipids we can directly address the function and contents of ceramic vessels. Here we present preliminary results of our research project aimed at addressing the function of Beaker pottery through organic residue analyses. Surprisingly, no support is found for the interpretation of Beakers as vessels used in alcohol consumption, and their very status as prestige items might even be questioned.

Melanie Pruvost et al
Nuclear ancient DNA draws picture of wild and early domesticated horses

Domesticated horses played key roles in the history of mankind providing nutrition and offering unprecedented modes of transportation. If the reasons related to the beginning of horse domestication are still unknown, horses were crucial to the life of nomadic pastoralists on the Eurasian steppe and had always have a particular position among domestic animal (warfare capabilities, symbol of social status, human's nutrition). For these reasons, deciphering the spatial and temporal origin of domestic horses is of key importance for understanding the origin of modern human societies. Due to the high variability of mtDNA among modern and ancient horse populations, the genetic analysis failed to reveal either time or place of horse domestication. In this case, the failure has pushed us to look for other genetic markers and to adapt new sequencing methods to ancient DNA. Thus, we were able for the first time to address the question of horse domestication by analyzing nuclear trait markers directly linked to early breeding practice. Coat color is an easily detectable phenotypic trait, which was likely a major goal of animal breeders since the beginning of domestication. Fortunately, single mutations are often responsible for color variants, which make these mutations very valuable for the analysis of SNP via pyrosequencing. We successfully typed for a dozen nuclear markers in more than 90 horse samples from the Pleistocene to medieval times. Through this example, we will present the advantage and limits of our methodological approach. By comparing mtDNA data and the data for coat color selection of horses, we will open the discussion about the perspective of the analysis of nuclear markers in palaeogenetics.

Linus Girdland Flink et al.
The Mediterranean route: analysing early domestic pigs in Southeast Neolithic France by combining Mitochondrial and Nuclear DNA with Geometric Morphometrics

The Neolithisation of Europe followed two main routes of expansion – the northern so called Danubian or Balkanic route and the southern Mediterranean route. Previous research has shown that the earliest domestic pigs in Europe were of Near Eastern descent, and specifically, that the spatiotemporal occurrence of haplotype Y1-6A is well correlated with the Danubian expansion. Whether domestic pigs along the southern route carried the same or divergent haplotypes remains unknown. A current hypothesis argues that early domestic pigs in the northern Mediterranean basin carried a different haplotype but has up to date lacked sufficient data to test it.

Here we report the results of our analysis of an 80bp d-loop fragment, a MC1R SNP that’s causative of dominant black coat colouring, and 2D geometric morphometric (GMM) data from sus remains in early to middle Neolithic layers in southeast France. Our results support the current hypothesis that divergent mitochondrial lineages accompanied the different routes of expansion as we find high prevalence of the Near eastern haplotype Y2-5A, but not a single Y1-6A. By applying GMM shape analysis we can show that individuals that carried a European d-loop signature (Aside haplotype) were significantly differentiated from individuals that carried the Y2-5A haplotype. This could imply a diverse origin that might represent local wild boar and imported domestic pigs. However, at least one individual that belonged to a European mitochondrial lineage also carried a derived allele at the 0301 locus in the MC1R gene – an allele that is assumed to have originated in domestic stock. Combined with previously published data, these results indicate that by 4000 BC, introgression with wild boar was widespread in Europe. For future analyses we aim to apply the integrated use of DNA and GMM to archaeological wild and domestic pig remains from locations across Europe and the Near East. As we demonstrated here, different analytical techniques can be used to answer a variety of questions and their combined use will make small case studies like this one more easily incorporated into a larger framework.

Ben Krause-Kyora et al.
The flying pig, migration or transfer of ideas in prehistory. Molecular genetic and archaeological investigations of Mesolithic and Neolithic pigs (Sus scrofa).

This study shows the reflection of population dynamics, like mobility and migration, in archaeological evidence from pigs. How did the domestication of the pigs take place in Northern Europe? Did domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic or did local European wild boar were also domesticated by this time?

First goal of this study was the development and establishment of extraction methods suited for extraction of DNA from historical samples, the selection of suitable genetic markers, and the establishment of sensitive, reliable and reproducible detection methods. PCRs were established to amplify pig-specific DNA with high sensitivity down to single molecules. Different primer pairs were used to amplify and sequence highly variable regions of the mitochondrial DNA like the dloop, cytb, XXX to determined specific mtDNA haplotypes. Further on specific nuclear DNA were analysed to determine the sex and the paternal haplotypes. The sequences finally aligned and compared to those already deposited in databases. A SNP analyse were established to determine the coat colour.

The results of over 300 individuals from 25 neolithic sites shows that around 4800- 4000 BC domestic pigs are introduced in the archaeological sites in northern Germany. The study points out that the oldest domestic pig in the sample (4600 BC) has a “Near East” haplotype. All other domestic and wild boars show the same “European” haplotype. The conclusion leads to the opinion that the domestic pigs with a maternal “Near East” ancestor were introduced into central Europe with the linear pottery (LBK) culture. After a short period the domestic pigs with “European” haplotypes coexist with the “Near East” haplotypes in the LBK and the Chaseen culture. An explanation could be that the people of the Ertebølle culture adapt the idea of domestication and permuted it on the indigenous wild boar population. With the established methods it is possible to determine the sex and the coat colour of ancient individuals. Further on the study shows the important of the coat colour as a marker for the domestication.

Josef Caruana & Terry Brown
The Maltese through time: A comparison of prehistoric, Roman and modern Maltese mitochondrial DNA haplotypes

The Maltese islands are a small archipelago situated in the middle of the Mediterranean Sea. Throughout history these islands have been dominated by the Mediterranean power of the era due to their strategic importance in controlling the shipping lanes between the eastern and western Mediterranean Sea. This study compares ancient DNA amplifications from a prehistoric site situated on the island of Gozo, two Roman burial sites in Malta, one of which is found in an urban context whilst the other in a rural context, and a sample group from the modern Maltese population. By analysing mitochondrial DNA Hypervariable Region 1, due to its higher copy number and survivability, this project aimed to study if any changes to the population of the islands can be observed through time. Another aim of the study was to see if any unique haplotypes might have survived these colonisations, and might still be present in the modern population. The modern Maltese population was also compared with other modern populations in the region in order to ascertain who it is most closely related to, and thus, which neighbouring influence most closely affected the matrilineal line of the Maltese population.

Origin of pig breeds

Molecular Biology and Evolution, doi:10.1093/molbev/msp118

INTEGRATING Y-CHROMOSOME, MITOCHONDRIAL AND AUTOSOMAL DATA TO ANALYSE THE ORIGIN OF PIG BREEDS

O. Ramírez et al.

Abstract

We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. While West African pigs from Nigeria and Benin exclusively harboured European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favoured the introduction of Far Eastern breeds into this continent.

Link

Middle Eastern origin of Neolithic pigs

Via the BBC Pig DNA reveals farming history:

Between 6,800-4,000 BC, farming methods spread across Europe, but the question of how these methods spread has not been fully established.

The two competing theories are that farming spread through cultural exchange, possibly during trading or that people migrated to Europe bringing their expertise with them.

A previous study, in 2005, analysed modern pig DNA and showed that all modern pigs are descended from European wild boar. This led researchers to conclude that early Europeans domesticated pigs independently of other farming methods.

This new study, however, has discovered that the first domesticated pigs in Europe did have Near Eastern ancestry, indicating that farmers migrated to Europe, bringing their "package" of livestock and farming methods with them.

Domestic pigs of European wild boar ancestry appear soon afterwards.