September 24, 2010

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.


Katharós said...

Interestingly the "paper" of the Neolithic graveyard from JEBEL AL-BUHAIS “BHS18” "United Arab Emirates" makes a similar statement.

Page. 160
The BHS 18 postcranial indices show a relatively close affinity to Linear Bandceramic series excavated in Germany, which date 5th and 6th millennium BC. However, earlier and later series from Viesenhäuser Hof vary considerably. The differences might be explained by migration.(Wahl and Burger-Heinrich, personal communication.)

Onur Dincer said...

What does it mean "with respect to the Balkans"? In order to estimate Central Asian genetic contribution to Anatolia, Anatolian Turkish genes should also be compared with Anatolian Greeks, Armenians and Kurds and also with the eastern neighbors of Anatolia, not just with the Balkans. But a much better method is ancient DNA tests and this has never been done in Anatolia in a large scale. Only large-scale spatial-temporal studies done in Anatolia so far are craniofacial studies; they pointed to strong genetic continuity in Anatolia at least since Neolithic times, especially in the maternal line, but that isn't conclusive as craniofacial studies are limited in their ability to detect small gene flows. A large-scale spatial-temporal DNA study would be much more conclusive.

Andrew Oh-Willeke said...

I'm particularly struck by the ancient pig DNA studies because they provide an line of evidence pretty much independent of the ancient human DNA, the physical anthropology of the remains, and the traces of material culture left behind, while telling essentially the same migration narrative. It matches the timing of the European Neolithic, supports the Daunubian LBK v. Southern Mediterranean divide, supports Near Eastern/Balkan origins for the LBK group, and shows how long it took for that population to become more integrated with their surroundings which is on the order of what is found by other means.