Where pastoralist met farmer and East met West (Spengler et al. 2014)

The paper's conclusion:

Archaeobotanical data from Central Eurasian pastoralist campsites have major implications for our understanding of late prehistoric agriculture across Asia. Sites like Tasbas and Begash illustrate the earliest acquisition of domesticated crops by mobile pastoralists and illustrate their capacity to participate in exchanges that bridged East Asian and Central Asian farming cultures by the early third millennium BC. Mobile pastoralists living in (southern) Central Asian alluvial fans and along the mountainous spine of Central Eurasia also integrated farming into their own domestic strategies (at least) by the mid second millenniumBC. Their pastoral mobility and the formation of extensive networks throughout the IAMC helped spread particular grain morphotypes and a mixed plant cohort of wheat, barley, millet and green peas through the mountains between Xinjiang, China and southwest Asia in the second millennium BC. The seasonal campsites of Begash, Tasbas, Ojakly and Site 1211/1219 are the earliest sites thus far reported to break down the strict polarization between nomads and farmers in prehistoric Central Eurasia. They also transform our comprehension of the vast arena of interaction that defines this region in ancient times. 

Related:

• Frachetti on the multiregional emergence of mobile pastoralism
• Horse not important for the emergence of steppe pastoralism
• Michael Frachetti on the Inner Asian Mountain Corridor

Proc. R. Soc. B doi:10.1098/rspb.2013.3382

Early agriculture and crop transmission among Bronze Age mobile pastoralists of Central Eurasia

Robert Spengler et al.

Archaeological research in Central Eurasia is exposing unprecedented scales of trans-regional interaction and technology transfer between East Asia and southwest Asia deep into the prehistoric past. This article presents a new archaeobotanical analysis from pastoralist campsites in the mountain and desert regions of Central Eurasia that documents the oldest known evidence for domesticated grains and farming among seasonally mobile herders. Carbonized grains from the sites of Tasbas and Begash illustrate the first transmission of southwest Asian and East Asian domesticated grains into the mountains of Inner Asia in the early third millennium BC. By the middle second millennium BC, seasonal camps in the mountains and deserts illustrate that Eurasian herders incorporated the cultivation of millet, wheat, barley and legumes into their subsistence strategy. These findings push back the chronology for domesticated plant use among Central Eurasian pastoralists by approximately 2000 years. Given the geography, chronology and seed morphology of these data, we argue that mobile pastoralists were key agents in the spread of crop repertoires and the transformation of agricultural economies across Asia from the third to the second millennium BC.

Link

Haplogroup E and Afroasiatic

This is an open access article.

European Journal of Human Genetics advance online publication 26 March 2014; doi: 10.1038/ejhg.2014.41

Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism

Eyoab I Gebremeskel and Muntaser E Ibrahim

Archeological and paleontological evidences point to East Africa as the likely area of early evolution of modern humans. Genetic studies also indicate that populations from the region often contain, but not exclusively, representatives of the more basal clades of mitochondrial and Y-chromosome phylogenies. Most Y-chromosome haplogroup diversity in Africa, however, is present within macrohaplogroup E that seem to have appeared 21 000–32 000 YBP somewhere between the Red Sea and Lake Chad. The combined analysis of 17 bi-allelic markers in 1214 Y chromosomes together with cultural background of 49 populations displayed in various metrics: network, multidimensional scaling, principal component analysis and neighbor-joining plots, indicate a major contribution of East African populations to the foundation of the macrohaplogroup, suggesting a diversification that predates the appearance of some cultural traits and the subsequent expansion that is more associated with the cultural and linguistic diversity witnessed today. The proto-Afro-Asiatic group carrying the E-P2 mutation may have appeared at this point in time and subsequently gave rise to the different major population groups including current speakers of the Afro-Asiatic languages and pastoralist populations.

Link

Lactase persistence and pastoralism in Africa

AJHG doi:10.1016/j.ajhg.2014.02.009

Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

Alessia Ranciaro et al.

In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa.

Link

Diverse occupants of Hungarian kurgan

Antiquity Volume: 86 Number: 334 Page: 1097–1111

Immigration and transhumance in the Early Bronze Age Carpathian Basin: the occupants of a kurgan

Claudia Gerling

You never know until you look. The authors deconstruct a kurgan burial mound in the Great Hungarian Plain designated to the Yamnaya culture, to find it was actually shared by a number of different peoples. The Yamnaya were an influential immigrant group of the Late Copper Age/Early Bronze Age transition. The burials, already characterised by their grave goods, were radiocarbon dated and further examined using stable isotope analysis on the human teeth. The revealing sequence began with a young person of likely local origin buried around or even before the late fourth millennium BC—a few centuries before the arrival of the Yamnaya. It ended around 500 years later with a group of different immigrants, apparently from the eastern mountains. These are explained as contacts built up between the mountains and the plain through the practice of transhumance.

Link

Khoisan genetic prehistory (Pickrell et al. 2012)

This appears to be the first paper using the specialized Affymetrix chip, which was announced some time ago, and used in some of my previous experiments. The new array has been dubbed "Affymetrix Human Origins array" and has been composed by intersecting panels of SNPs ascertained in individuals from several world populations.

It is of course great to see that this paper has appeared as a preprint in arXiv, and hopefully this is a trend that will continue; biology should be like physics, with papers appearing immediately online for commenting, and not hidden away in authors', editors', and reviewers' drawers for months if not years before they become available to all.

I will highlight some points of particular interest to me:

Some caveats of interpretation here are warranted. First, all the Khoisan populations have some level of admixture with non-Khoisan populations. There is thus no single \split time" in their history, and any method (like the one used here) that estimates a single such time will actually be estimating a composite of several signals. Second, we have made the modeling assumption that history involves populations splitting in two with no gene  ow after the split. More complex demographies are quite plausible, but render the interpretation of a split time nearly meaningless (if populations continue to exchange migrants after \splitting", they arguably have not split at all). We thus consider strong interpretations of split times estimated from genetic data to be impossible, but we nonetheless and the estimates to be useful in constraining the set of historical hypotheses that are consistent with the data. 

This echoes (somewhat) my sentiments about split times being a tug-of-war in the presence of admixture. Another interesting bit from the paper:

Interestingly, a few of the Khoe-speaking populations have slightly positive f4 statistics in this com- parison, and in the Shua the f4 statistic is significantly greater than zero. We speculate that some of the Khoe-speaking populations have a low level of east African ancestry, and that the relevant east African population was itself admixed with a western Eurasian population. The Shua also show a detectable signal of admixture LD, though we estimate the admixture date as much older (44 generations). This signal of east African ancestry specifically in Khoe-speaking populations is of particular interest in the light of the hypoth esis that the Khoe-Kwadi languages were brought to southern Africa by a pre-Bantu pastoralist immigration from eastern Africa [Guldemann, 2008] 

The authors also announce an improvement on TreeMix:

In the original TreeMix algorithm, one first builds the best-tting tree of populations. However, this approach is not ideal if there are many admixed populations (as in our application here, where all of the Khoisan populations are admixed). To get around this, we allow for known admixture events to be incorpo- rated into this tree-building step. Imagine that there are several populations that we think a priori might be unadmixed (in our applications, these are the Chimpanzee, Yoruba, Dinka, Europeans, and East Asians). We  first build the best tree of these unadmixed populations using the standard TreeMix algorithm. Now assume we have an independent estimate of the admixture level of each Khoisan population, and imagine we know the source population for the mixture. 

I don't think that Sub-Saharan African populations can any longer be considered unadmixed. When one used SNPs ascertained in Eurasian individuals, many Sub-Saharan populations appear symmetrically related to Eurasians, because they lack variation at sites where new polymorphism appeared outside Africa. 

This is not, however, the case when one uses SNPs ascertained in African individuals, and a clear pattern of differential affiliation with West Eurasians across the continent is evident. As I have said before, I strongly suspect that this is due to fairly late back-migration of Eurasians into Africa, carrying Y-haplogroup DE chromosomes. Within haplogroup CT, both its major subclades CF and DE are represented in Eurasia, and both D,E, and DE* as well. In Africa, as far as we know, only DE* and E are native. On balance, the weight of the evidence would suggest a Eurasian origin of the DE-YAP haplogroup.

(I would perhaps be as bold as to extend this into the even more basal clades of the phylogeny which turn up with surprising regularity in Eurasian datasets, and are usually discounted as the result of recent admixture. I'm not so sure; if recent admixture was at fault, then the African signal in Eurasia would be absolutely dominated by E-related lineages: but the A's and B's turn up in quite unexpected places. Are they really all recent Africans, or could they share a much deeper common ancestry? If I had deep pockets, I'd surely invest in genome sequencing the collection of such Eurasian erratics)

As a parting thought, I hope that the data used in this paper will become publicly available in time, perhaps when the article appears in journal form. True open science depends not only in the public availability of research results, but also of the data that produced them.

UPDATE: Here is the ADMIXTURE analysis from the paper (Figure 7):

It would have been nice if the Fst values between ancestral populations were reported in the paper; also, if an East Eurasian group was added in the analysis. In any case, there does appear a pattern of differential affiliation with the French population (K=2). At K=3 the main Sub-Saharan (blue) component emerges, and a few populations continue to exhibit an excess of West Eurasian affiliation.

arXiv:1207.5552v1 [q-bio.PE]
The genetic prehistory of southern Africa

Joseph K. Pickrell et al.

The hunter-gatherer populations of southern and eastern Africa are known to harbor some of the most ancient human lineages, but their historical relationships are poorly understood. We report data from 22 populations analyzed at over half a million single nucleotide polymorphisms (SNPs), using a genome-wide array designed for studies of history. The southern Africans-here called Khoisan-fall into two groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. All individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began 1,200 years ago. In addition, the Hadza, an east African hunter-gatherer population that speaks a language with click consonants, derive about a quarter of their ancestry from admixture with a population related to the Khoisan, implying an ancient genetic link between southern and eastern Africa.

Link

Frachetti on the multiregional emergence of mobile pastoralism

I had previously posted on horses not being important for the emergence of steppe pastoralism, in which Frachetti and Benecke documented how the early (4,500ky) Begash culture of Kazakhstan had developed full-blown pastoralism without apparently relying on horses.

This is in contradistinction to both the Botai culture where there is abundant evidence for horse use, apparently for food, as well as the Eneolithic cultures of the European steppe where horse bones are much more prevalent than in early Begash.

The simple model of the emergence of pastoral nomadism proposes the spread of this mode of subsistence from the European (Pontic-Caspian) steppe, together with horses and horse-drawn vehicles. Popularized by David Anthony in recent years, this model views horses and wheels as the great enablers of pastoralism, and views the emergence of pastoral cultures across the steppe as the result of movements of mobile pastoralists -atop their horses, and with their herds- across the Eurasian steppe.

Frachetti is a critic of this model, and proposes instead the importance of the (hitherto neglected) Inner Asian Mountain Corridor as important in facilitating prehistoric contacts between east and west. In a new paper in Current Anthropology he elaborates on his proposed "multiregional" model of the emergence of mobile pastoralism.

I have not read the paper's 38 pages carefully yet (including CA comments and response), but this is clearly a seminal work on the studied topic that will be referenced for years to come. I will post any specific comments in updates to this post. For the moment, I will limit myself to a couple of observations:

• Recent work in Y-chromosome phylogeny has established a fairly disjoint division within haplogroup R1a1a; in particular the R-Z93 subhaplogroup seems to abound in the "Asian steppe", as well as Asia in general, while being generally absent in Europe; the R1a1a and Subclades Y-DNA Project is keeping track of new developments in this field.
• My own research on autosomal DNA, suggests the confluence of two "streams" of ancestry onto the steppe: a west-to-east stream emanating from eastern Europe, and associated with the Atlantic_Baltic (K7b) or North_European (K12b) ancestral component; as well as a West_Asian (K7b) or Caucasus/Gedrosia (K12b) component emanating from the highland regions south of the Caspian and south of the steppe (the traditional Silk Road territory).

These lines of evidence certainly appear to be consistent with a "multiregional" model of early mobile pastoralism. In particular they testify to the non-uniformity of ancestry of steppe groups and are inconsistent with their derivation from a single source. The picture is further complicated by the historical movements of nomads across the steppe (including Scytho-Sarmatian type people as well as Turkic-Mongolian ones). Charting the emergence of steppe populations will require a great deal of sleuthing in the genomes of modern steppe inhabitants, as well as a great deal of work on ancient DNA.

In any case, the new paper by Michael Frachetti will provide important new insight to all those who seek to understand "what actually happened" in Eurasian prehistory, and it is a very welcome addition to the ongoing debate.

Current Anthropology Vol. 53, No. 1, February 2012

Multiregional Emergence of Mobile Pastoralism and Nonuniform Institutional Complexity across Eurasia

Michael D. Frachetti


Abstract

In this article I present a new archaeological synthesis concerning the earliest formation of mobile pastoralist economies across central Eurasia. I argue that Eurasian steppe pastoralism developed along distinct local trajectories in the western, central, and (south)eastern steppe, sparking the development of regional networks of interaction in the late fourth and third millennia BC. The “Inner Asian Mountain Corridor” exemplifies the relationship between such incipient regional networks and the process of economic change in the eastern steppe territory. The diverse regional innovations, technologies, and ideologies evident across Eurasia in the mid-third millennium BC are cast as the building blocks of a unique political economy shaped by “nonuniform” institutional alignments among steppe populations throughout the second millennium BC. This theoretical model illustrates how regional channels of interaction between distinct societies positioned Eurasian mobile pastoralists as key players in wide-scale institutional developments among traditionally conceived “core” civilizations while also enabling them to remain strategically independent and small-scale in terms of their own sociopolitical organization. The development of nonuniform institutional complexity among Eurasian pastoralists demonstrates a unique political and economic structure applicable to societies whose variable political and territorial scales are inconsistent with commonly understood evolutionary or corporate sociopolitical typologies such as chiefdoms, states, or empires.

Link

Pastoral and farmer populations from the Sahel

In Central Asia, the expansion of the Mongol nomads led to the predominance of a few Y-chromosome lineages of relatively recent vintage. The opposite seems to be true for the African pastoralists examined here: they see to be more diverse in their Y-chromosomes than farmers are, and less so in their mtDNA. This suggests that they were a fairly old group who did not particularly marry farmers' daughters.

Mol Biol Evol (2011) doi: 10.1093/molbev/msr067

Genetic structure of pastoral and farmer populations in the African Sahel

Viktor Černý et al.

Traditional pastoralists survive in but few places in the world. They can still be encountered in the African Sahel, where annual alternations of dry and wet seasons force them to continual mobility. Little is known about the genetic structure of these populations. We present here the population distribution of 312 HVS-I mtDNA and 364 Y-STR haplotypes in both farmer and pastoralist groups from the Lake Chad Basin and the West African Sahel. We show that the majority of pastoral populations (represented in the African Sahel by the Fulani nomads) fail to show significant departure from neutrality for mtDNA as evidenced by Fu's Fs statistics, and exhibit lower levels of intra-population diversity measures for mtDNA when contrasted with farmers. These differences were not observed for the Y chromosome. Furthermore, AMOVA analyses and population distributions of the mtDNA haplotypes show more heterogeneity in the sedentary groups than in the pastoralists. On the other hand, pastoralists retain a signature of a wide phylogenetic distance contributing to their male gene pool, whereas in at least some of the farmer populations a founder effect and/or drift might have led to the presence of a single major lineage. Interestingly, these observations are in contrast with those recorded in Central Asia, where similar comparisons of farmer and pastoral groups have recently been carried out. We can conclude that in Africa there have been no substantial mating exchanges between the Fulani pastoralists coming to the Lake Chad Basin from the West African Sahel and their farmer neighbors. At the same time we suggest that the emergence of pastoralism might be an earlier and/or a demographically more important event than the introduction of sedentary agriculture, at least in this part of Africa.

Link

More Uniform Sampling of Human Genetic Diversity (Xing et al. 2010)

Some observations on the paper:

New World populations (Totonac and Bolivian) are placed between Nepalese and Kyrgyzstanis, indicating higher affinity of these American samples to central Asians than to eastern Asians.

This is more likely an artifact of the mixed (Caucasoid-Amerindian) ancestry of these American samples, rather than an indication of their Central Asian origin, as the authors seem to believe. This is an important caveat, as American Indians and Central Asians are "pulled together" by their shared West Eurasian ancestry of post-Columbus and Neolithic/Chalcolithic Age origin respectively, and correspondingly "pulled away" by Mongoloids proper from East Asia who lack that admixture.

Polynesians also deviate from East Asians towards Europeans, less strongly than Central Asians, and this reflects low-level admixture between ancestral Polynesians and colonial-era Europeans.

The Eurasian PCA is interesting:

At the sub-continental level, we focus first on Eurasia, where most of our samples have been selected (Figure 4A). Overall, PC1 and PC2 mainly reflect the geographic distribution of the populations, with the majority of genetic variation accounted for by their locations. PC1 (accounting for 62.7% of the variance) reflects an east-west gradient, while PC2 (3.3% of the variance) reflects a north-south gradient.

There is absolutely no reason (based on geographical distance) for PC1 to account for twenty times more variance than PC2. PC1 reflects the racial contrast between Caucasoids and Mongoloids, while PC2 reflects the much weaker latitudinal adaptation and south-to-north spread of humans into the higher latitudes.

Another thing to notice is how tightly clustered Caucasoids are, from the Atlantic to Iraq (a distance of about 4,000km), which is -conservatively- about half the distance between Pakistan and South India. This is due to the fact that South Asians were formed by admixture of two elements: an extraneous Caucasoid one and an indigenous Paleo-Indian one. Notice also that this variable admixture (highest Caucasoid component in Brahmins) is not really compatible with an indigenous origin of the caste system, as has been proposed on non-scientific grounds.

More spread (given geographical distance) is also observed in Central Asia and Southeast Asia, and this is explained by relatively recent admixture between Caucasoids and Mongoloids (in the former) and Paleo-Indian-like morphological "Australoids" and Mongoloids (in the latter).

The results of ADMIXTURE analysis (for Eurasian individuals) are presented in graphical format in the paper itself, for (K=7).

Not much to comment on this that hasn't been seen before:

One observation is the existence of some "red" West Asian component in the N. European sample, which is not found in Slovenians. This may parallel the peculiarity of the Caucasoid components observed for Russians and Lithuanians recently, although the several Caucasoid components detected in that study are folded into 2 in the current one.

Notice also, how "red" is the main extraneous component in Indian Brahmins. As expected, even Brahmins are predominantly of "indigenous" origin, as these Brahmins are from Tamil Nadu and Andhya Pradesh, and not from North India. The West Asian affiliations of the main Caucasoid component are evident, and agree with Behar et al. (2010) where South Asians had a major overlap with West Asians (light green) and a minor one with Europeans (dark blue). In this paper, with a lower K the different European and West Asian subclusters are not visible.

The most interesting part of the study -for me- was the inclusion of three novel African samples, the Luhya, Alur, and Hema. Notice the blue component in these people, which resolves partially to orange at K=12. This is an indication of Eurasian affinities that are mostly lacking in other black Africans.

The Luhya are Bantu speakers from Kenya, so they are not indigenous to East Africa, but have probably picked up some native East African ancestry from their non-Bantu neighbors.

The Hema are from the Democratic Republic of Congo, but they are Nilo-Saharan pastoralists. Their fairly noticeable West Eurasian component may reflect origins outside the Congo. Are these another member of the non-Bantu pastoralists expanding from East Africa to the south? It would be interesting to take a look at these people's Y chromosomes.

All in all, a very interesting paper which adds important new populations to the discussion of human origins. Also of note, the free availability of the paper's genotype data and supplementary material at the Jorde Lab.

Genomics doi:10.1016/j.ygeno.2010.07.004

Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping

Jinchuan Xing et al.

High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~ 250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (FST) substantially decreases from ~ 16% with the HapMap II samples to ~ 11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations.

Link

Soil and climate as economic destiny

Figure 1 (on the left) Modelled “suitability” (probability of occurrence, Maxent) for (A) agriculture, (B) sedentary animal husbandry, (C) nomadic pastoralism, and (D) hunting and gathering.

From the paper:

Our simplistic exercise showed that a “geo-deterministic” approach can predict surprisingly many features of human cultural geography without any explicit cultural or historical assumptions. Although many deviations require further factors for a satisfying explanation, the nature of these deviations invite the generation of hypotheses for further research. Our ‘null model’ offers a highly parsimonious, empirically supported explanation to the question of why some regions are more “powerful” than others, supplementing the idea of a historical effect operating through the timing of transition to agriculture [2].

In some instances, our model may actually provide a simpler explanation. Putterman [10], for example, suggested that the dominance of Western European cultures indicates the transmission of “civilization” traits (other than knowledge on agriculture) from regions of first domestication. Our data indicate that higher climatic suitability may have been sufficient for Europe to “catch up”, allowing for much higher population densities than, e.g., the “fertile crescent” region. Models of “suitability” under past climatic scenarios may be helpful to evaluate this. Similarly, models applied to predicted future climatic scenarios may be useful to anticipate changes of the economic suitability of landuse types.

However, our model has clear deviations in some regions that may well be explicable by the availability of animals and plants suitable for domestication (e.g., central Africa). Apart from that, and more importantly, we know that human societies and economies went through historical development, so ignoring history may not always be the best strategy to understand causalities. This problem occurs also with other research questions in biogeography, e.g. when investigating global biodiversity patterns [45]–[47]. Nevertheless, our ‘null model’ will be a useful tool in identifying regions that require further investigation to understand additional processes that shape the distribution and performance of human economic traits.

I really like this type of paper that looks at a simple explanation for a phenomenon, in this case, economic output as a product of soil/climate quality and suitability. As the authors point out, their "null" model has its limitations, and it is precisely in regions of the world where its predictions do not match the observations, that we should look for additional factors (besides soil and climate) to explain economic traits.

Related: Soil and Greek temples.

PLoS ONE 5(5): e10416. doi:10.1371/journal.pone.0010416

Is the Spatial Distribution of Mankind's Most Basic Economic Traits Determined by Climate and Soil Alone?

Jan Beck, Andrea Sieber

Abstract

Background
Several authors, most prominently Jared Diamond (1997, Guns, Germs and Steel), have investigated biogeographic determinants of human history and civilization. The timing of the transition to an agricultural lifestyle, associated with steep population growth and consequent societal change, has been suggested to be affected by the availability of suitable organisms for domestication. These factors were shown to quantitatively explain some of the current global inequalities of economy and political power. Here, we advance this approach one step further by looking at climate and soil as sole determining factors.

Methodology/Principal Findings
As a simplistic ‘null model’, we assume that only climate and soil conditions affect the suitability of four basic landuse types – agriculture, sedentary animal husbandry, nomadic pastoralism and hunting-and-gathering. Using ecological niche modelling (ENM), we derive spatial predictions of the suitability for these four landuse traits and apply these to the Old World and Australia. We explore two aspects of the properties of these predictions, conflict potential and population density. In a calculation of overlap of landuse suitability, we map regions of potential conflict between landuse types. Results are congruent with a number of real, present or historical, regions of conflict between ethnic groups associated with different landuse traditions. Furthermore, we found that our model of agricultural suitability explains a considerable portion of population density variability. We mapped residuals from this correlation, finding geographically highly structured deviations that invite further investigation. We also found that ENM of agricultural suitability correlates with a metric of local wealth generation (Gross Domestic Product, Purchasing Power Parity).

Conclusions/Significance
From simplified assumptions on the links between climate, soil and landuse we are able to provide good predictions on complex features of human geography. The spatial distribution of deviations from ENM predictions identifies those regions requiring further investigation of potential explanations. Our findings and methodological approaches may be of applied interest, e.g., in the context of climate change.

Link

Bronze Age origin of Semitic languages

Bayesian phylogenetic methods, originally developed for biology, have been increasingly -and successfully- applied to linguistic data in recent years (e.g., for Indo-Europeans, Melanesians, and Austronesian speakers from the Pacific).

The current paper proposes a Bronze Age origin for Semitic languages, ~3 thousand years after the split of European from Anatolian Indo-European speakers. I don't find this particularly surprising, as Semitic has been, until relatively recently, much more geographically constrained than Indo-European, and -due to the early literacy of the populations of the Near East, its post-Neolithic arrival can be observed in the archaeological record itself.

It also explains a facet of Y-chromosome distribution, that I have commented on before, namely the fact that the common Near Eastern haplogroup J2 extends from Europe to South Asia in a "horizontal zone" accompanied with little of its sister clade J1, but in the Near East itself, there is a "vertical zone" from the Black and Caspian seas to Arabia of high J1 frequency. As I have explained recently, the mixed J2/J1 frequency in the central Near East is due to an enrichment with J1 lineages of a population that had (in pre-Semitic times) a high J2/J1 ratio like those of Europe, Asia Minor, and Iran. J1 should not be seen as exclusively Semitic, but it can't be denied that the major factor affecting its current spread has been the arrival of Semites from the South, the latest episode of which involved the spread of Arab Muslims.

The current study also demonstrates that linguistic Bayesian phylogenetics (LBP) has no inherent bias to produce older dates for language dispersals; while the origin of the Indo-European (IE) language family has been dated to the early European Neolithic, and now Semitic to ~6,000 years, the spread of Melanesian languages to Pleistocene times, and of the Austronesian settlement of the Pacific to ~5,000 years. The congruence between LBP and traditional archaeology in all these cases should force IE exceptionalists who cling to the old theory of "steppe horse riders" to explain why, only in the dispersal of IE, it should LBP should have failed.

The paper also has free supplementary data, including a multistate phylogeny (pdf) of Semitic languages (reproduced top left of this post).

(More details to follow after I thoroughly read the paper)

UPDATE (Aug 27):

From the paper:

Furthermore, Eblaite (no Eblaite wordlists were available for our study), the closest relative of Akkadian and the only other member of East Semitic, was spoken in the Levant (specifically the northeast Levant or present-day Syria; Gordon 1997), which is also where some of the oldest West Semitic languages were spoken (Ugaritic, Aramaic and ancient Hebrew). The presence of ancient members of the two oldest Semitic groups (East andWest Semitic) in the same region of the Levant, combined with a possible long interval (100–3000 years) between the origin of Semitic and the appearance of Akkadian in Sumer, suggests a Semitic origin in the northeast Levant and a later movement of Akkadian eastward into Mesopotamia and Sumer (see figure 1 for a map of our proposed Semitic dispersals).

An origin of Semitic in northeast Levant (Syria) would be consistent with the observed east-west cline of decreasing J1 frequency in the Levant; the authors do, however, mention that the possibility for unknown extinct languages of the Semitic language may shift both the age of the language and its place of origin.

Lacking closely related non-Semitic languages to serve as out-groups in our phylogeny, we cannot estimate when or where the ancestor of all Semitic languages diverged from Afroasiatic. Furthermore, it is likely that some early Semitic languages became extinct and left no record of their existence. This is especially probable if early Semitic societies were pastoralist in nature (Blench 2006), as pastoralists are less likely to leave epigraphic and archaeological evidence of their languages.

A pastoralist association of Semitic languages is also consistent with the observed correlation of haplogroup J1 with herders and J2 with settled farmers in the Near East.


Proc. R. Soc. B 7 August 2009 vol. 276 no. 1668 2703-2710

Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East

Andrew Kitchen et al.

Abstract

The evolution of languages provides a unique opportunity to study human population history. The origin of Semitic and the nature of dispersals by Semitic-speaking populations are of great importance to our understanding of the ancient history of the Middle East and Horn of Africa. Semitic populations are associated with the oldest written languages and urban civilizations in the region, which gave rise to some of the world's first major religious and literary traditions. In this study, we employ Bayesian computational phylogenetic techniques recently developed in evolutionary biology to analyse Semitic lexical data by modelling language evolution and explicitly testing alternative hypotheses of Semitic history. We implement a relaxed linguistic clock to date language divergences and use epigraphic evidence for the sampling dates of extinct Semitic languages to calibrate the rate of language evolution. Our statistical tests of alternative Semitic histories support an initial divergence of Akkadian from ancestral Semitic over competing hypotheses (e.g. an African origin of Semitic). We estimate an Early Bronze Age origin for Semitic approximately 5750 years ago in the Levant, and further propose that contemporary Ethiosemitic languages of Africa reflect a single introduction of early Ethiosemitic from southern Arabia approximately 2800 years ago.

Link

Retroviruses and the Origin of domesticated sheep

This paper suggests an "early" dispersal of sheep from the Near East, relics of which exist in peripheral areas, and a secondary major dispersal, also from the Near East, which is responsible for most modern sheep breeds.

Remnants of the earlier sheep breeds tend to have lower-quality wool, and this suggests that the secondary dispersal of sheep was associated with the beginning of the exploitation of the sheep's fur, rather than only its meat, resulting in the popularity of the new breeds.

It will be extremely exciting to track this dispersal archaeologically. We ought to have a few diagnostic SNPs of the various breeds of all the major domesticated animals very soon, which would be relatively easy to amplify in archaeological bone samples.

From the paper:

Collectively, the data we obtained indicate that relicts of the first migrations are still present in the Mouflon of Sardinia, Corsica, and Cyprus and in breeds in peripheral north European areas.

...

The homogeneous retrotypes (R2 only, or both R2 and R4) that we observed in the sheep of modern-day Turkey, Iran, Saudi Arabia, Syria, Israel, and Egypt, combined with available archaeological evidence, suggest that selection of domestic sheep with the desired secondary characteristics common to the modern breeds occurred first in Southwest Asia and then spread successfully into Europe and Africa, and the rest of Asia. [...] The primitive breeds survived the second migrations of improved breeds from Southwest Asia by returning to a feral or semiferal state in islands without predators or by occupying inaccessible areas less prone to commercial exchanges and associated introgression.

...

Our study also provides genetic evidence supporting the anecdotal origin of some less common sheep breeds. For example, one of the 10 populations analyzed from the British Isles, the Jacob sheep, displayed a homogeneous R2 retrotype very different from that of the other British populations and more similar to that of the southwestern Asiatic and African breeds [...] Our study also firmly links the Soay sheep with the Mediterranean and Asiatic Mouflon.

Science doi:10.1126/science.1170587

Revealing the History of Sheep Domestication Using Retrovirus Integrations

Bernardo Chessa et al.

Abstract

The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their "retrotype" and morphological traits dispersed across Eurasia and Africa via separate migratory episodes. Relicts of the first migrations include the Mouflon, as well as breeds previously recognized as "primitive" on the basis of their morphology, such as the Orkney, Soay, and the Nordic short-tailed sheep now confined to the periphery of northwest Europe. A later migratory episode, involving sheep with improved production traits, shaped the great majority of present-day breeds. The ability to differentiate genetically primitive sheep from more modern breeds provides valuable insights into the history of sheep domestication.

Link

Genome of cattle breeds

The part I put in bold is interesting, as humans are themselves a "self-domesticated" species.

From the paper:

Our high resolution examination of cattle shows that unlike the dog—which has restricted diversity and high levels of inbreeding—domesticated cattle had a large ancestral population size and that more aurochs must have been domesticated than wolves; reducing the severity of the domestication bottleneck. SNP diversity within taurine breeds was similar to that of humans, but was significantly less than diversity within indicine breeds, which suggested that the Indian subcontinent was a major site of cattle domestication and predomestication diversity. Selection first for domestication and then for agricultural specialization have apparently reduced breed effective population sizes to relatively small numbers.

Related:

• Y chromosomes of Neolithic cattle do not suggest hybridization with European aurochsen
• Paleogenetics of cattle domestication

Science doi:10.1126/science.1167936

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The Bovine HapMap Consortium

Abstract

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

Link

Later Stone Age South African Hunter gatherers and Herders as a single population

Related regarding a pastoralist migration to South Africa: Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa.

Journal of Archeological Science doi: 10.1016/j.jas.2008.11.001

Craniometric evidence for South African Later Stone Age herders and hunter-gatherers being a single biological population

Deano D. Stynder

Abstract

Later Stone Age (LSA) hunter-gatherers and herders co-existed in South Africa during the last 2,000 years. In spite of being the focus of intensive research over the years, the biological status and origins of the herders are still unclear. Did they represent a genetically distinct immigrant population who remained separate from the indigenous hunter-gatherers, or where they indigenous hunter-gatherers who took up herding after contact with herders, probably in northern Botswana? Here, this issue is investigated using craniometric data collected on a large sample of individually dated human crania from coastal LSA context. Mahalanobis distances (D), calculated from the raw metric data, show that there was a small increase in inter-individual craniofacial variation after the introduction of herding at c. 2,000 BP. Here it is argued that this small increase in variation is neither consistent with a largescale immigration of genetically distinct herders into South Africa, or the long-term coexistence of two genetically distinct populations. Two alternative explanations fit the data better: (1) herding entered South Africa via the small-scale immigration of genetically distinct herders; and (2) local hunter-gatherer populations adopted herding after coming in contact with herders in northern Botswana. While small-scale immigration would not have had a major influence on the local gene pool, it would have increased variation to some extent as immigrants mixed with local populations. If small-scale external gene flow was not a factor in the introduction of herding, secular issues related to the introduction of herding could explain the increased variation in post-2,000 BP populations.

Link

Central Asian patrilineal populations

On the same topic as the preceding post. I would add that a major cause for the higher informativeness of the human Y-chromosome is the fact that most of the presently dominant lineages in the world are fairly recent, and hence there has been less time for random diffusion of patrilineages on the map to wipe out pre-established patterns of Y-chromosomes associated with archaeologically or historically dominant patriarchal groups.

In the standard model, males are more static, and females more mobile, because they may move fairly long distances to settle in their husband's residence. This factor is counterbalanced, I think, by the excess organized migration of surplus males in societies where there is socio-economic/reproductive inequality.

Thus, the constant individualistic short-range migration of women, coupled with their greater reproductive equality, over long periods of time, evens out the distribution of mtDNA lineages, with the resulting distribution further obscured by (climate-related) selective factors acting on human mtDNA. On the contrary, the Y-chromosome landscape is established by patrilocal males staying by and defending their hearths, but is occasionally punctuated by long-range collective migration of patrilineally related males.

PLoS Genetics doi:10.1371/journal.pgen.1000200

Sex-Specific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study

Laure Ségurel et al.

Abstract

In the last two decades, mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome (NRY) have been extensively used in order to measure the maternally and paternally inherited genetic structure of human populations, and to infer sex-specific demography and history. Most studies converge towards the notion that among populations, women are genetically less structured than men. This has been mainly explained by a higher migration rate of women, due to patrilocality, a tendency for men to stay in their birthplace while women move to their husband's house. Yet, since population differentiation depends upon the product of the effective number of individuals within each deme and the migration rate among demes, differences in male and female effective numbers and sex-biased dispersal have confounding effects on the comparison of genetic structure as measured by uniparentally inherited markers. In this study, we develop a new multi-locus approach to analyze jointly autosomal and X-linked markers in order to aid the understanding of sex-specific contributions to population differentiation. We show that in patrilineal herder groups of Central Asia, in contrast to bilineal agriculturalists, the effective number of women is higher than that of men. We interpret this result, which could not be obtained by the analysis of mtDNA and NRY alone, as the consequence of the social organization of patrilineal populations, in which genetically related men (but not women) tend to cluster together. This study suggests that differences in sex-specific migration rates may not be the only cause of contrasting male and female differentiation in humans, and that differences in effective numbers do matter.

Link

New Y-chromosome haplogroup E-M293 unites most of E-M35* (and how not to correlate archaeology with genetics)

This study makes two contributions:

First, it reports the discovery of a new major clade within the Y-chromosome phylogeny which unites many previously paraphyletic E-M35* chromosomes, and charts its distribution in Africa (left).

The second claim in the study is that this new clade is associated with the spread of pastoralism into southern Africa:

Using the same mutation rate described in Fig. 1, we estimated a maximum age of 2,700 ya (ρ=0.6, n = 10) with a standard error (SE) of 1,100 y.

...

A major unresolved question is: were early instances of sheep, cows, pottery, and their pastoralist markers transmitted to southern-central Africa by demic or cultural diffusion?

...

Given the directionality and dating discussed previously, we conclude that eastern African individuals contributed M293 to southern African populations within the last few thousand years. The scale of this migration may have been small, minimally four male individuals

But, this claim is another house of cards based on an assumption of an evolutionary mutation rate that is much lower than the observed germline rate. The authors cite Zhivotovsky et al. (2004) (pdf) regarding this rate, but Zhivotovsky, Underhill, and Feldman (2006) showed that such a lower effective rate is observed in a constant-sized population, where each lineage grows stochastically according to a Poisson process with parameter 1. The expected number of its descendants after g generations is 0.5g or 40 individuals after 2,000 years, a few orders of magnitude less than the real number of E-M293 bearers.

So, the evolutionary rate is totally inappropriate for the pastoralist groups in question who have grown to a much larger size than that.

For a more thorough discussion of the problems with the evolutionary rate, see my two part discussion (part I and part II). In a group that expands in size a much faster evolutionary rate is appropriate, approaching the germline rate.

The argument that E-M293 is associated with the introduction of pastoralism to southern Africa is another house of cards resting on the assumption of the slow evolutionary mutation rate.

So, while E-M293 did follow the proposed migration route, and E-M293 migrants were also pastoralists, they weren't necessarily the people who introduced pastoralism to southern Africa -- they came much later.

Related public release and blog post at the Spittoon.

PNAS doi: 10.1073/pnas.0801184105

Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa

Brenna M. Henn et al.

Abstract

Although geneticists have extensively debated the mode by which agriculture diffused from the Near East to Europe, they have not directly examined similar agropastoral diffusions in Africa. It is unclear, for example, whether early instances of sheep, cows, pottery, and other traits of the pastoralist package were transmitted to southern Africa by demic or cultural diffusion. Here, we report a newly discovered Y-chromosome-specific polymorphism that defines haplogroup E3b1f-M293. This polymorphism reveals the monophyletic relationship of the majority of haplotypes of a previously paraphyletic clade, E3b1-M35*, that is widespread in Africa and southern Europe. To elucidate the history of the E3b1f haplogroup, we analyzed this haplogroup in 13 populations from southern and eastern Africa. The geographic distribution of the E3b1f haplogroup, in association with the microsatellite diversity estimates for populations, is consistent with an expansion through Tanzania to southern-central Africa. The data suggest this dispersal was independent of the migration of Bantu-speaking peoples along a similar route. Instead, the phylogeography and microsatellite diversity of the E3b1f lineage correlate with the arrival of the pastoralist economy in southern Africa. Our Y-chromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa ≈2,000 years ago.

Link

Correlation of Y-haplogroups J2 and J1 with Neolithic agro-pastoral economies

Roy King and Peter Underhill had previously published on the Congruent distribution of Neolithic painted pottery and ceramic figurines with Y-chromosome lineages, in which they found that:

Only the Eu9 [Dienekes: J2-M172] haplogroup successfully predicted the distribution of both Neolithic figurines (88% accuracy) and painted pottery (80% accuracy).

From the paper:

Lifestyle differences exist between agriculturalists and pastoralists (Khazanov 1984). Sedentary agriculturalists and semi-nomadic herders often occupy different ecological niches (Cauvin 2000; Zarins 1990). Dry farming without irrigation is confined to regions of
250-400mm of annual precipitation (Bar-Yosef 1998; Buccellati 1992), while pastoral nomadism is an adaptation to regional semi-aridity (Bellwood 2005; Zarins 1990). It has been shown that the spatial variation of rainfall is important in dictating the structure of endemic flora (Kadmon & Danin 1999). Since the focus of our study is the Neolithic transition, we restrict our analysis of Y-chromosomes and rainfall to the approximate Fertile Crescent ‘homeland’ region implicated in the shift to an agro-pastoralist economy.

...

As predicted, both haplogroups J1 and J2a correlated significantly with annual precipitation. The Spearman correlation tests gave the following results for each haplogroup: J1 r= −0.45, p<0.05; J2a r=0.56, p<0.01; and J2b r=0.00, p (not significant) ... As shown, haplogroup J1
frequency increases as precipitation level reduces below the 400mm per year threshold, typical of semi-arid climates. In contrast, haplogroup J2a frequency reaches a maximum at 700mm per year within the Mediterranean woodland and open parkland zone (Bar-Yosef 1998).

I wonder how these results would change if populations from the Caucasus were included where there are some very significant J1 concentrations that seem to exceed even those of Semitic speaking groups except the Arabians. It's not clear how related the J1 found in places like Daghestan is to that of the Arabian peninsula, or if it resembles the J1 with the short DYS388 alleles found in northeastern Anatolia (where there is high precipitation). Perhaps just as J2a (but not J2b) correlates with high precipitation, a yet-to-be-discovered subclade of J1 is a stronger signal linked to arid climates.

I have been thinking about J1/J2 distribution in West Asia recently; the early surveys of its variation suggested a north/south Fertile crescent dichotomy between the two, but now its distribution looks more like a cross (+) or a T, with a longitudinally constrained J1-rich zone from Arabia to the eastern Caucasus, crossed by a east-west J2-rich zone across the length of the Anatolian peninsula (and indeed into southern Europe) on the west side, and Iran, Pakistan, and India on the east side. What is strange is that both westward and eastward from the central region (the middle point of the +, places like Iraq, eastern Turkey, Syria, northern Iran) the J2/J ratio decreases, approaching ~0.9 in the Balkans, and really 1.0 on the opposite side among the J1-less Hindus.



Antiquity Volume: 82 Number: 316 Page: 281–289

Correlation of annual precipitation with human Y-chromosome diversity and the emergence of Neolithic agricultural and pastoral economies in the Fertile Crescent

Jacques Chiaroni1, Roy J. King and Peter A. Underhill

Examining the beginnings of agriculture in the ‘Fertile Crescent’, this research team has compared the distribution of rainfall with the distribution of Y-chromosome haplogroups. The extended families signalled by J1 and J2 haplogroups seem to have had different destinies in the era of agro-pastoralist experiment: J2 were the agricultural innovators who followed the rainfall, while J1 remained largely with their flocks. Acknowledging the fuzzy edges of such mapping, the authors nevertheless escort us into new realms of the possible for the early history of peoples.

Link

ISBA3 abstracts

Many abstracts from the International Symposium on Biomolecular Archaeology.

Various DNA / Technology

Human ancient DNA analysis within The Genographic Project: a project update and preliminary results from two powerful multiplex SBE typing methods

Wolfgang Haak1, Juan J Sanchez2, Clio Der Sarkissian1, Christina Adler1 & Alan Cooper1

1 The Australian Centre of Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia
2 National Institute of Toxicology and Forensic Science, Canary Islands Delegation, 38320 Tenerife, Spain.

The Australian Centre of Ancient DNA (ACAD) is one of 11 Regional Centres of The Genographic Project (TGP), and the only centre dedicated solely to ancient human DNA analyses. Our aim is to provide a temporal perspective to the movements and presence of prehistoric and historic populations through ancient DNA, and establish a time depth to the detailed genetic landscape being generated from the largescale modern human population data of TGP. We will present an update on the current activities and an overview of the protocols and strategies used in the ACAD. The retrieval of authentic human ancient DNA is plagued by methodological problems, and to deal with these we are relying on state-of-the-art methods ranging from sample collection through to data generation. We are using SPEX and multiplex PCR assays followed by SBE typing to analyse both mtDNA coding region markers and nuclear NRY markers. New multiplex assays were designed to amplify highly degraded DNA with an average amplicon length of 60-80bp, targeting 22 mtDNA SNPs and 25 NRY SNPs - to match the core marker panel used within TGP. Preliminary results show that the SBE typing protocols are robust and prove to be highly efficient in targeting minute amounts of suriving aDNA. In addition, the main advantage of SBE has proven to be the detecting power of omnipresent (background) contamination. We conclude that the mtDNA and NRY SBE assays, in combination with sequence data from the mtDNA control region (backed up by cloning and SPEX), and specialised sample collecting systems, provide a powerful means to effectively generate largescale (pre-)historic population data from ancient human samples.

What colour was Attila the Hun’s horse?: genetic signatures of phenotypic traits in archaeological materials

Mim A. Bower¹, Michael G. Campana², Diane Lister¹, Mark Whitten³, Kathy M. Dominy⁴, Angela M. Murphy⁵, Paula Jenkins⁶, Richard Sabin⁶, Michael Akam⁷, Robert Asher⁷ & Matthew Binns⁵.

¹ McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.

² Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK.

³ Comparative Population Linguistics Group, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.

⁴Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, SE1 9RT, UK.

⁵Department of Veterinary Basic Sciences, the Royal Veterinary College, Royal College Street, London, NW1 0TU, UK.

⁶ Department of Zoology, Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK

⁷Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.

Studying the phenotype, i.e. what a plant or animal looked or behaved like, is perhaps the next “Holy Grail” in ancient DNA research. If we could trace the genes responsible for particular characters in archaeological specimens, it would open the door to some highly relevant and interesting questions in archaeology; the least of which may be the elusive “domestication gene”, but could cover more basic questions, such as: did people in mediaeval Europe prefer cows that had a tendency to lay down fat or muscle? When and where did a particular genetic disorder enter a domestic population? Was the spread of agriculture influenced by adverse environmental conditions? Or what colour was Attila the Hun’s horse? We could begin to understand past approaches to animal and plant husbandry, the expression of past human choice and selection, and past understanding of biological processes such as heredity. Fortunately, molecular biology is fast uncovering the genes responsible for particular phenotypic traits – the only problem, and a significant one perhaps, is looking for these genetic signatures in ancient DNA, known to be a recalcitrant material for analysis.

Here we present the results of our research on phenotypic loci in various historic and archaeological materials (bones, teeth, parchment, hide, seeds), and discuss the potential for future of phenotypic research in archaeogenetics.

Greece & Italy

Aristophanes and Stable Isotopes: Comparing literary and isotopic evidence of diet in Classical Thebes, Greece.

Efrossini Vika ^1,2, Mike Richards^3,4, Holger Schutkowski² and Vassilis Aravantinos⁵

¹ School of Conservation Sciences, Bournemouth University, BH12 5BB, UK

² Division of Archaeological, Geographical and Environmental Sciences, University of Bradford, BD7 1DP, UK

³ Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, DE

⁴ Department of Archaeology, Durham University, DH1 3LE, UK

⁵ IX Ephorate of Prehistoric and Classical Antiquities, Thebes 60200, GR

The greatest advantage for an archaeologist working with historically dated material is the existence of literary sources, which can complement scientific analyses in archaeology. The present study compiles a dietary profile for the inhabitants of Classical Thebes, using δ¹³C and δ¹⁵N isotope analysis, comparing this evidence with information on diet as presented in Aristophanes’ comedies (Acharnians, Plutus, Wasps).

Aristophanes’ work is abundant in satirical scenes, which emphasize personal attributes and local characteristics. Within this realm, it is possible to extract information on dietary habits, trade and economy in the Classical times. Merchants from Thebes oftentimes appear in his work, reflecting the city’s wealth. Among the goods deriving from this region, eels feature prominently, and are praised as an exceptional delicacy.

Stable isotope analyses of bone collagen were carried out for individuals from the Classical burials of the Northeastern cemetery of Thebes. Results show a remarkable increase of the nitrogen values relative to the previous periods, which is not accompanied by an analogous enrichment of the carbon values. This profile can partly be explained by an increased consumption of freshwater sources in Thebes during the Classical times, such as Aristophanes’ famous eels.

The results demonstrate how the integration of isotopic and literary evidence can provide novel information about Classical society in Thebes.

Greek myths

Terry Brown
Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK

The Greek Bronze Age is the time of the Homeric legends and the Greek myths. The work of Schliemann, Tsountas, Wace and others revealed the material remains of the Mycenaean civilisation that was dominant in the Aegean during the 17th to 12th centuries BC, these remains including human skeletons, some buried with rich grave goods. Biomolecular archaeologists have been attracted to the Greek Bronze Age because there are interesting kinship questions for the burials at several sites, and because aDNA could throw light on the impact of diseases such as malaria on these societies. Addressing these questions clearly requires that aDNA is preserved in the relevant material, and our conclusion after ten years of work is that largely it is not. We have found no indication of aDNA at Lerna, Antron Grave Circles A and B and Mycenae Grave Circle A. At Mycenae Grave Circle B, we detected mitochondrial aDNA in just four of the 22 skeletons that we studied. Only at Kouphovouno have we have obtained sufficient aDNA results to attempt any kind of archaeologically relevant study. The distinguishing feature of Kouphovouno is that we obtained skeletal samples immediately after their excavation. We used optimised PCR systems in order to maximise our chances of detecting aDNA if it was present, but we also used a high containment facility and took scrupulous care to remove surface contamination from the bone samples and to prevent cross-contamination with PCR products from previous experiments. We also confirmed that our negative results were not due to inhibition of PCRs by substances co-purifying with aDNA. Negative results tend not to get widely publicised – we would have preferred positive ones but not if they lead to new Greek myths.

Late Bronze Age Diet in the Greek Peloponnese

E.I.Petroutsa1 & M.P.Richards2

1.20 Koundouriotou str., Exarcheia, 10683 Athens, Greece

2.Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany


In this paper we present the results of an isotopic study of bone collagen samples from four Late Bronze Age cemeteries from the Northern Peloponnese in Greece: Voudeni, Aghia Triada, Almyri and Kritika. Through isotope analyses we sought to characterise the general diets in these four sites, especially the amounts of marine protein, as well as animal vs. plant proteins in diets. We also compared the isotopic results from these sites with other Bronze Age sites, including Mycenae. Despite the coastal location of most of the sites we could not find evidence of any significant consumption of marine foods. Instead, most human diets are based on a mixture of plant and animal protein, from C3 terrestrial resources.

Preliminary results of C and N isotope analyses and 14C dating of prehistoric humans and animals from the Mesolithic-Neolithic site of Grotta dell’Uzzo, Sicily, Italy

Marcello A. Mannino1, Sahra Talamo1, Rosaria Di Salvo2, Vittoria Schimmenti2, Marcello Piperno3, Sebastiano Tusa4, Antonio Tagliacozzo5, Michael P. Richards1,6

(1) Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig (Germany)

(2) Museo Archeologico Regionale ‘Antonino Salinas’, Via Bara all’Olivella 24, 90133 Palermo (Italy)

(3) Dipartimento di Scienze Storiche, Archeologiche ed Antropologiche dell’Antichità, Sezione di Paletnologia, Università di Roma ‘La Sapienza’, Via Palestro 63, 00185 Roma (Italy)

(4) Soprintendenza del Mare, Palazzetto Mirto, Via Lungarini 9, 90133 Palermo (Italy)

(5) Museo Nazionale Preistorico Etnografico ‘L. Pigorini’, Piazzale Guglielmo Marconi 14, 00144 Roma E.U.R. (Italy)

(6) Department of Archaeology, University of Durham, South Road, DH1 3LE Durham (United Kingdom)

Grotta dell’Uzzo is one of the key sites in the Mediterranean for the study of the changes in subsistence that took place in the transition from hunter-gatherer (Mesolithic) to agro-pastoral (Neolithic) economies. The cave is also important because 13 Mesolithic humans have been unearthed from 11 burials excavated within it. In order to study the diets of these humans, C and N isotope analyses were undertaken on skeletal remains recovered in the burials and from different trenches excavated at the cave. The preliminary results of these analyses suggest that the main sources of dietary protein were terrestrial and probably originated from the consumption of mammalian herbivores such as red deer (the most commonly exploited animal for much of the cave’s occupation). The contribution of marine resources to human diet at Grotta dell’Uzzo was probably not very significant in absolute terms. This finding might appear to be in contrast with the results of the archaeozoological studies, which have demonstrated that there was an intensification in shellfish collecting and in fishing from the end of the Mesolithic to the inception of the Neolithic. However, given that on the basis of the chronological data currently available the burials predate the end of the Mesolithic, the results of the isotope analyses are in line with the findings of the archaeozoological studies and of the seasonality studies, which have shown that marine resources (mainly represented by shellfish) were not exploited throughout the year before the final stages of the Mesolithic.

Plants

Phylogeographic analysis of barley (Hordeum vulgare) landraces shows that the distribution of lineages retains an imprint from the initial patterns of agricultural spread through Europe.

Huw Jones1, James Cockram1, Lydia M Smith1, Ian MacKay1, Robin G Allaby2, Terrence A Brown3, Wayne Powell1

1 National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE

2 Warwick HRI , Wellesbourne, Warwick , CV35 9EF

3 Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN

In the 8000 years since barley was first introduced into the continent of Europe, the evolution of this crop species has been subject to selection under biotic and abiotic pressures. European farmers will have influenced the distribution of barley ecotypes by the movements of early farmers and by their selection of preferred types. The evolution of barley in Europe will also reflect the differing environments in which it has been grown. Modern barley cultivars from across Europe can be seen to differ in their morphology and growth habits. We have attempted to dissect the origins of these different forms by examining the landraces and assess the relative importance of human and environmental selection on modern barley lineages.

We have sampled barley landraces from Europe and discovered their population structure by microsatellite genotyping and statistical analysis. We have used passport data from germplasm collections to characterise the 2-row / 6-row head morphology, hulled / naked grain morphology and the spring / winter growth habit of these sub-populations. The genetic variation underlying key adaptive traits controlling flowering time has been explored by re-sequencing the photoperiod response gene Ppd-H1 and by haplotype analysis at the spring / winter vernalisation genes Vrn-H1 and Vrn-H2. These studies were designed to run alongside analysis of ancient DNA and historic DNA from barley and emmer wheat collected from across Europe.
The population structure we have discovered divides barley landraces into a number of sub-populations each with a distinct geographic distribution. Our genetic data for key adaptive traits allows us to understand the environmental influence on the geographic distribution of each lineage. Where lineages with a similar adaptive profile have distinct geographic distributions we see the imprint of early dispersal by ancient farmers.

Stable isotope evidence for the consumption of millet in Bronze Age Italy

Mary Anne Tafuri1, Oliver Craig2 & Alessandro Canci2
1 Dipartimento di Biologia Animale e dell’Uomo, Sapienza Università di Roma, P.le A. Moro, 5, 00185 Roma. Italy – email: maryanne.tafuri@uniroma1.it

2 Department of Archaeology, University of York, BioArch Biology, S Block PO Box 373 York YO10 5YW, UK

3 Dipartimento di Storia e Tutela dei Beni Culturali, Università degli Studi di Udine, Via Palladio, 8, 33100 Udine. Italy


This study presents, via carbon and nitrogen stable isotope analysis on human and animal bone collagen, new data on diet and subsistence strategies at northern and southern Italy Early and Middle Bronze Age sites, which clearly indicate the direct or indirect consumption of C4 plants. On the basis of paleobotanic data available and as suggested by previous similar studies, we argue here that the isotopic signal obtained can be associated with the consumption of millet (P. miliaceum and Setaria italica). If such an interpretation were true, while we wait for further paleobotanical and isotopic studies, we should consider the results obtained as the earliest evidence of millet consumption in prehistoric Europe. We thus suggest a possible pattern of distribution in the Peninsula of the practice of production and consumption of millet, while setting a new agenda on food security and subsistence strategies in prehistoric Italy

Cattle & Goats

A PCR system free of contaminating DNA for the amplification of bovine DNA from bovine fossils

Camille Berthelot, Sophie Champlot, Marie Liouville, Thierry Grange, Eva-Maria Geigl

Institut Jacques Monod CNRS UMR 7592, Universités Paris 6 et 7, Tour 43, 2, Place Jussieu, 75251 Paris cedex 05, France

Palaeogenetic analyses of bovine bone remains from many Neolithic sites in Europe and in Southwest Asia suffer from poor DNA preservation in these bones that increases the risk of amplification of contaminating modern bovine DNA. Indeed, trace amounts of contaminating bovine DNA occur ubiquitously. In particular, they can be found at low quantities in biochemical reagents used to extract and amplify DNA. These contaminating molecules mimic ancient DNA molecules. Indeed, the contamination rate often resembles the success rate of ancient DNA studies from bovine remains and the length of the contaminating DNA fragments is often comparable to ancient DNA fragments. We elaborated a decontamination protocol for PCR reagents combining various treatments to reduce contamination towards zero. This system significantly increases the reliability of ancient DNA results from bone remains of domesticated animals.

Detecting selection in ancient cattle remains: Pre industrial selection in Bos Taurus and SNP typing in medieval cattle remains

Emma Svensson1, Anders Götherström1

1 Evolutionary Biology, Evolution Genomics & Systematics, Uppsala University, 752 36 Uppsala, Sweden

Historic and prehistoric animal breeding is an enigmatic topic, complicated to approach with conventional genetics and osteology. Questions like when it started, and how strict it was, are of general interest, but it is also complicated to generate a suitable dataset for such questions. By tracing changes in genetic diversity with serial data we can find out how cattle has changed since the domestication of the aurochs to become the array of breeds seen today. Cattle are likely to have been subjected to selection predating the 18th century but the information is scarce. Using a 12plex SNP stream system alongside pyrosequencing we typed up to eight coding and six neutral SNPs in 142 ancient and 216 modern Bos Taurus from Northern Europe. We found a significant decrease in total heterozygosity over time for the coding SNPs which are presumably associated with phenotypic traits such as milk quality and coat colour while neutral markers on the other hand don’t show any significant change over time. This suggests that the decline in diversity is caused by artificial selection and not other genetic processes. The medieval period was a dynamic time in northern European history. The society was moving toward a higher degree of specialization in general, and a number of towns based on trade arouse in Scandinavia. Our findings of early selection fit well with the more sophisticated farming and higher degree of animal breeding that likely occurred at this time.

Using new and old approaches to study bovid systematics and evolution across Eurasia

Alan Cooper¹, Kefei Chen¹, Beth Shapiro²

¹ The Australian Centre of Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia

² Department of Biology, The Pennsylvania State University, 326 Mueller Laboratory, University Park PA 16802, USA

Ancient DNA studies of bovid remains from Europe have detected four main taxa: Bison bonasus (the European Bison); Bison priscus (Steppe bison), Bos primigenius (Aurochs); and early Bos taurus (Daisy). Studies of bones recovered from caves in the Urals and Caucasus, and from material dredged from the North Sea, have revealed a fifth European bovid – the Caucasus bison. Previously recognised only as a sub-species of European bison, this taxon appears to represent a separate species, with more genetic diversity than Beringian populations of Bison priscus, suggesting a long evolutionary history and stable population size. It has changed ecological dominance with Bison priscus at several points in the Pleistocene, which appear to be related to climatic and environmental change.

We have been using emulsion PCR and high-throughput hybridisation-based SNP screening systems that can simultaneously analyse 50,000 bovid SNPs to explore the genomic evolution of ancient bovids during the Pleistocene and subsequent domestication. We have been concentrating on pre-domestic Bos taurus specimens, as well as representatives of the other Pleistocene bovid species. This approach holds enormous promise for fine-scale temporal analyses of evolution in response to climate and environmental change, as well as archaeology and domestication.

The process of cattle domestication during the Neolithic as revealed by a large-scale palaeogenetic study

Eva-Maria Geigl, Mélanie Pruvost, Marie Liouville, Camille Berthelot, Reinhard Schwarz, Sophie Champlot, Thierry Grange, Virginia Bessa-Correia, Hans-Peter Uerpmann, Lamys Hachem, Hitomi Hongo, Séverine Braguier

Institut Jacques Monod CNRS UMR 7592, Universités Paris 6 et 7, Tour 43, 2, Place Jussieu, 75251 Paris cedex 05, France

Several disciplines can contribute to the elucidation of the processes of animal domestication during the Neolithic, such as archaeology, archaeozoology, and, more recently, isotope and genetic studies. The processes of domestication leave genetic signatures in the genomes of the domesticated animals that can be explored via the combination of both genetic analyses of extant domesticates and palaeogenetic analyses of bone remains of the first generations of domesticated animals and of their wild ancestors. We adopted this approach to shed light on the domestication of the aurochs. We studied roughly 250 Bos bone remains from Southwest Asia, according to archaeological and archaeozoological evidence the presumed centre of cattle domestication, and from France, the region where the two Neolithic migration currents mingled. To obtain authentic palaeogenetic results, several methodological difficulties related to poor DNA preservation and reagent contamination had to be solved. We will present both the methodological challenge that we encountered and overcame and the results of our large-scale study.

Cattle domestication and the troublesome aurochs

Cecilia Anderung1, Jurgita Baubliene2, Daniel Makowiecki3, José Miguel Carratero4, Linas Daugnora2, Juan Luis Arsuaga5 and Anders Götherström6

1Palaeontology Department, Natural History Museum, Cromwell road, London SW7 5BD, Great Britain.
2Department of Anatomy and Histology, Lithuanian Veterinary Academy, Tilžes str. 18, LT-3022, Kaunas, Lithuania
3Institute of Archaeology, Nicolaus Copernicus University, Podmurna 9/11 87-100 Toruń, Poland
4Laboratorio de Evolución Humana, Departamento Ciencias Históricas y Geografía Edificio I+D+I Plaza de Misael Bañuelos s/n, 09001, Burgos, Spain
5Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos c/ Sinesio Delgado Nº 4 Pabellón 14, 28029 Madrid, Spain
6Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden

A number of genetic studies relating to the origin of modern cattle have been published recently. In particular the extinct European aurochs (Bos primigenius), progenitor of the modern domesticated form, has attracted a lot of attention. European aurochs bones that have yielded mitochondrial DNA are genetically clearly different from modern cattle. This genetic data, in combination with the genetic patterns observed in modern cattle, has led to the suggestion that modern cattle have a single origin in the Near East, and that the European aurochs population had little to do with their domestication.

However, we ask the question: could this picture of European cattle domestication be too simple?

Here we present results from an investigation of published and novel aurochs sequences from Lithuania, Spain, Poland, and Britain, giving special attention to the Spanish sequences. We looked at the mitochondrial DNA variation in Iberian aurochs remains and searched for aurochs sequences in a domestic context. We find that cattle and aurochs mitochondrial sequences from Iberia deviate from the pattern observed in sequences from Central and Eastern Europe.

In the light of this data, we discuss the possibility of local aurochs domestication events in Europe.

High mtDNA diversity among cattle and goats from the earliest Neolithic settlements on the European continent

Amelie Scheu1,2, Norbert Benecke2 and Joachim Burger1
1 AG Palaeogenetik, Institut für Anthropologie, Johannes Gutenberg-Universität, 55099 Mainz, Germany

2 Deutsches Archäologisches Institut, Eurasienabteilung, 14195 Berlin, Germany

The process of domestication includes a decline in genetic variability. Additional homogenisation occurs due to subsequent colonisation events, such as the Neolithisation of Europe. Our previous studies have shown genetic uniformity even among early Neolithic European cattle (Bollongino et al. 2006). But modern goats also share more than 90% of the same mtDNA haplogroup.

To find out exactly when and where this genetic bottleneck arose during the Neolithisation of Central Europe, we investigated remains of early domesticates on the border between Asia and Europe, i.e. at the origin of the trans-Danubian route of Neolithisation. That region, particularly the area around the Bosphorus and the transit country of Bulgaria, plays a crucial role.

We found higher mtDNA diversity among Neolithic and Bronze Age domesticated cattle East and West of the Black Sea (haplogroups T, T2 and T3) than in Central European populations. Among goats, we found the two different mtDNA haplogroups A and G. G had previously been found among modern goats only near the Fertile Crescent (Naderi et al. 2007).

Our results argue for large and genetically more diverse herds imported to this area and/or for intense trade. Furthermore, they indicate that a second wave of expansion in the direction of Central Europe is responsible for the final loss of mtDNA diversity.

Ice man Schnidi’s trousers: insight into prehistoric goat diversity

Angela Schlumbaum1, Serge Volken 2, Marquita Volken 3, Jörg Schibler4, Peter Suter 5 Kathrin Glauser6 & Albert Hafner 7

1 Institute of Prehistory and Archaeological Science, University of Basel, Spalenring 145, 4055 Basel, Switzerland

2 Gentle Craft, Rue du Rôtillion, 10, 1001 Lausanne, Switzerland

3 Gentle Craft, Rue du Rôtillion, 10, 1001 Lausanne, Switzerland

4 Institute of Prehistory and Archaeological Science, University of Basel, Spalenring 145, 4055 Basel, Switzerland

5 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland

6 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland

7 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland
Since 2003 more than 300 prehistoric remains were discovered in the vicinity of a melting ice patch of the Schnidejoch (2750 m; Bernese Alps, Switzerland), paralleling the finds accompanying the Iceman from the Tisenjoch (Oetztal Alps, Italy/Austria; “Oetzi”). One leg of a Neolithic leather trouser was found and 14C dated to 2900 – 2600 BC. The morphological identification of the animal skin was ambiguous because of the bad preservation of diagnostic features. Based on grain patterns of the skin the leather was made either from sheep or goat.

Because of the importance of the object, a genetic identification of the animal species was attempted. After DNA extraction with QiAmp DNA Mini Kit a 70bp fragment of the mitochondrial cytochrome b gene was amplified in the diluted extract. The leather was made of goat skin (Capra hircus). Six geographically broadly distributed goat lineages are recognized based on mitochondrial d-loop variation, of these lineage A and C were identified by others in prehistoric goat bones from France. The “trouser’s goat” however, belongs to lineage B, which is common in Asia, but extremely rare in Europe today.

An Ancient DNA study from The Farm Beneath the Sand

Martin Bay Hebsgaard1

1 Dept. of Biology, University of Copenhagen, Universitetsparken 15, Denmark
Applying ancient DNA techniques on samples from the archaeological site “The Farm Beneath the Sand” (GUS) near Nuuk in Southwest Greenland is the first attempt to extract DNA from these relative young but novel samples. The sample site highlight the dramatic landscape changes that resulted in floodplain aggradations that eventual buried the site fixing the site under perma-frozen conditions.
The Farm beneath the Sand is situated on a plain surrounded by low mountains ca. 80 km east of Nuuk. When the building remains were found they were overlain by ca. 1,5 m thick layers of sand and gravel, and today the plain in front of the farmhouse appears as a sandy dessert intersected by meandering watercourses that are draining off the icecap.

All together the samples yielded DNA from humans, cattle, sheep, goat and reindeer. Quantification shows approximately 16 times more DNA from cattle than from sheep. Goat DNA was undetectable using Quantitative PCR. The amount of cattle DNA declines over time while sheep DNA probably reflects background variation.
Thanks to thick layers of sand and gravel that may have protected the DNA in the anthropogenic layers ancient DNA is usable in an archaeological context in the reconstruction of the past. In this example ancient DNA research has helped to refine and define archaeological interpretations of the Norse life by adding information not seen by the naked eye. In the future ancient DNA have the capacity to be used more vigorously to investigate the diet of the Norse and show what function specific farms may have had during the settlement. As in this study the future research is not limited to animal DNA but DNA from plant and humans can be used to address different questions.

Horses

Pleistocene Horses genetics before and after the last glacial maximum

Sebastian Lippold¹ and Michael Hofreiter¹

¹ Dept. Evolutionary Genetics, MPI for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany

We are investigating how the last glacial period affected the genetic composition of populations, particularly the horse (Equus spec.). Vast climatic changes that occurred between 30,000 and 12,000 years BP resulted in dynamic mammalian population structures. Restriction and expansion events during this period influenced both the genetic distribution and variability of a variety of mammals. We focus on western European horse populations, and try to characterize their genetic diversity and phylogeographic patterns both before and after the last glacial maximum. We sequence 600 bp of mtDNA from the mitochondrial D-Loop of different individuals obtained from different locations. Our initial results indicate tremendous genetic diversity, but no phylogeographic pattern within this marker. The genetic distribution of these ancient samples also falls within the broad diversity range apparent in recent horses. Because of this finding, we started screening the DNA samples for additional nuclear markers. Our comparison of these different markers has enabled us to reconstruct several scenarios for horse population dynamics during this period.

Investigating Eneolithic horse exploitation in northern Kazakhstan, via compound-specific stable carbon and deuterium isotope analysis of pottery.

Natalie A. Stear1, David Chivall1, Alan K. Outram2 and Richard P. Evershed1 1Organic Geochemistry Unit, School of Chemistry, University of Bristol, Clifton, BS8 1TS, UK 2 Department of Archaeology, SoGAER, University of Exeter,Laver Building, North Park Road, Exeter, EX4 4QE, UK The Eneolithic site of Botai in northern Kazakhstan has been the centre of much debate regarding its role in early horse domestication (Levine, 1999; Olsen, 2003). The faunal assemblage from this remarkable site was almost entirely comprised of horse (99%); however it has remained unknown whether any of these horses were domesticated. Horse domestication is extremely difficult to detect morphologically from skeletal remains and consequently it is necessary to establish a reliable proxy for detecting ancient domestic horse populations. Fermented mare’s milk (Kumyss) is commonly consumed in rural communities in Kazakhstan, a tradition dating back to prehistory. It is not clear if the milking of horses began (i) in the Eneolithic, during the height of the horse centred communities of the Botai culture; (ii) in the Bronze Age, in response to the milking of ruminants or, (iii) much later. If mare’s milk were identified in ancient pottery it would serve as conclusive evidence for the presence of domestic horses and enable a chronology of horse exploitation to be established. Equine fat residues can be identified in potsherds using compound-specific stable carbon isotope analysis, but unlike ruminant fats, equine milk and adipose fats are indistinguishable from one another based on δ13C values. However, we show that it is possible to further classify equine fats as either milk or adipose, based upon the δD values of their C16:0 and C18:0 fatty acids which are determined using GC-thermal conversion-IRMS (GC-TC-IRMS). This new proxy has been applied to organic residues extracted from potsherds from Botai as part of a large scale investigation of Eneolithic and Bronze Age pottery from sites in northern Kazakhstan. Using the δ13C and δD values obtained from the Botai residues we have been able to detect equine milk residues preserved within the pottery and consequently, we provide the first direct evidence for the presence of domestic horses at Botai during the Eneolithic.

Anatolia

Detecting dairying with stable calcium isotope ratios (δ44/42Ca) of bones and teeth

Linda M. Reynard^1,2, Robert E.M. Hedges¹ & Gideon M. Henderson²

¹ Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, United Kingdom

² Department of Earth Sciences, University of Oxford, Parks Road, Oxford, OX1 3PR, United Kingdom

The use of dairy products in antiquity is an important part of the development of agriculture and pastoralism in Eurasia. They offer advantages of more efficient land use, improved nutrition, and more reliable and constant access to protein. Understanding the adoption of dairy, its timing, and geographical spread is relevant to developing a fuller understanding of changes in subsistence from the Neolithic.

Detecting and quantifying dairy product consumption in antiquity has, to date, relied on indirect evidence such as the age and sex structure of faunal remains and potsherd lipid residues.. To complement these methods, we have measured stable calcium isotope ratios (δ^44/42Ca) of bones and teeth which allows the direct detection of dairy consumption by prehistoric humans. Dairy products have lower δ^44/42Ca than other dietary calcium inputs, and this results in lower δ^44/42Ca of the dairy consumer. We have measured the δ^44/42Ca of human and animal bones from a range of archaeological sites by MC-ICP-MS. Results from the Mesolithic to the Neolithic at the key Near Eastern site of Abu Hureyra, Syria (11,100 –7,300 BP) show a δ^44/42Ca signal attributable to dairy consumption by ancient humans, with a changing pattern through time. Work on intra- and inter-tooth δ^44/42Ca variability is in progress as this material is expected to form a robust archive of in vivo isotope ratios.


Britain

An investigation into origins of individuals from a mass grave in Roman Gloucester, UK: strontium and stable isotope evidence

Carolyn Chenery^1,2, Gundula Müldner¹, Jane Evans², Louise Loe³, Nicholas Márquez Grant³, Hella Eckardt¹ Stephanie Leach¹, Mary Lewis¹

¹ Department of Archaeology, University of Reading, Reading, Berkshire.

² NERC Isotope Geoscience Laboratory, British Geological Survey, Keyworth, Nottingham.

³ Oxford Archaeological Unit Ltd, Janus House, Osney Mead, Oxford.

Contrary to popular assumptions, Britain under Rome was truly multi-cultural, with historical and epigraphic evidence recording the voluntary and forced migration of Gaulish, Germanic and North African individuals into the British provinces refs. This paper presents the results an isotopic investigation of population diversity in 1^st to the 4^th century Roman Gloucester; focusing on individuals found in a late 2^nd century mass burial pit and comparing them to those found in single graves.

The results suggest that the majority of the individuals buried in the London Road Cemetery were from areas within the UK. However, the isotope data has identified a number of individuals whose origins lay in a region with a warmer climate than the UK. Whether these were soldiers, their followers or merchants cannot be determined.

On Rome’s Northern Frontier: Multi-isotopic investigations into cultural diversity in Roman York

Gundula Müldner1, Carolyn Chenery1,2, Stephany Leach1, Mary Lewis1 & Hella Eckardt1

1 Department of Archaeology, University of Reading, Whiteknights, PO Box 227, Reading RG6 6AB, England

2 NERC Isotope Geoscience Laboratory, British Geological Survey, Keyworth, Nottingham, NG12 5GG, England

Britain under Rome was a multi-cultural society, with historical and epigraphic evidence attesting to the presence of migrants from continental Europe, North Africa and the Middle East. Here, we combine isotope analysis for the reconstruction of diet (C,N) and mobility (Sr, O) with skeletal (craniomorphometric) and archaeological data, in order to investigate diversity in Roman York, the political, military and administrative centre of the North. The results show a heterogenous population and highlight the varied life-histories of individuals in the northernmost provincial capital of the Empire; however, they also show that skeletal and isotopic evidence are not always easily correlated. It is suggested that a diet high in marine protein was used to demonstrate a “Roman” identity.

Investigating Marine Food Consumption in Prehistoric Humans via the δ13C values of Collagen Amino Acids

Philip Dunn1, Richard P. Evershed1 & C. Joshua Pollard2
1 School of Chemistry, University of Bristol, Organic Geochemistry Unit, School of Chemistry, Cantock's Close, Bristol, BS8 1TS, UK

2 Department of Archaeology and Anthropology, 43 Woodland Road, Clifton, Bristol BS8 1UU, UK

The current debate concerning the importance of marine foods in the diets of prehistoric peoples has stimulated interest in refining analytical approaches based on stable isotopes. An alternative to the widely bulk collagen approach is to investigate the stable carbon isotope composition of human bone collagen at the amino acid level. Our investigations of prehistoric humans from the Western Cape, South Africa, have shown that the Δ13CGlycine-Phenylalanine values for bone collagen amino acids correlate strongly with bulk δ15N values and provide a new proxy for marine food consumption. We are currently applying this new approach to human skeletal remains from northern Europe.
The tomb at Isbister lies on the south west coast of South Ronaldsay and is one of a number of Neolithic cairns found in the Orkney Islands. During excavation in 1976, the stalled main chamber and three side chambers were found to contain some 16,000 human bones and bone fragments deriving from a minimum of 341 individuals along with a wide range of faunal remains. Previous analyses of bone collagen from the human remains have shown that the tomb was in use from 4,500 to 3,800 BP and bulk collagen stable isotope values for 5 individuals lay in the range -19.9 to -21.2 ‰ indicating a predominantly terrestrial diet, which is surprising for people that lived so close to the coast.
We have now employed the recently introduced LC-IRMS technique to determine the δ13C values of bone collagen amino acids from 22 individuals from Isbister. The results will be compared to those obtained by GC/C/IRMS. The derived Δ13CGlycine-Phenylalanine values give enhanced insights into the dietary habits of the people of Isbister.

Northern Europe

Large-scale FLX-sequencing and the Swedish Neolithic

Helena Malmström1,2, Anna Linderholm3, M. Thomas P. Gilbert2, Mikael Brandström1, Jan Storå4, Petra Molnar4, Christian Bendixen5, Gunilla Holmlund6, Kerstin Lidén6, Anders Götherström1, Eske Willerslev2

1Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden

2Ancient DNA and Evolution Group, Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark

3Archeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

4Osteoarchaeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

5Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences Research Centre Foulum, K25 PO Box 50, DK-8830 Tjele, Denmark

6National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology, Artillerigatan 12, SE-587 58 Linköping, Sweden

The relationship between the contemporary hunter-gatherer Pitted Ware Culture (PWC) and the farming Funnel Beaker Culture (TRB) in Middle Neolithic (3300-2500 B.C.) Sweden has been debated for more than a century. We approach this issue by determining the genetic signatures of skeletal remains from both complexes. Initially, we generated large amounts of “cloned” ancient mitochondrial DNA (mtDNA) PCR amplicons using a single run of the Genome Sequencher FLX System, and a recently described primer tagging protocol. Our data set consisted of Hypervariable Region I (HVRI) amplicons derived from bleach pre-treated powdered bone from Neolithic humans as well as from a large number of negative controls (animal samples, extraction and PCR blanks). We compared the ‘clone’ data with sample quality indicators, such as the number of PCR starting template molecules and the degradation ratio of DNA in the sample (number of long/short fragments). The data shows distinct patterns that differ between high and low quality extracts. After establishing the efficacy of the large scale sequencing approach, additional high-quality PWC and TRB samples (based on collagen preservation) were sequenced in a second FLX run. The compiled data yielded unambiguous HVRI sequences for approximately 40 Neolithic human samples, each compiled from cloned, duplicate PCR amplicons derived from overlapping HVRI fragments. F-statistics and AMOVA revealed significant genetic differences between the PWC and TRB samples, indicating that they indeed comprise of two distinct groups.

Allele frequencies of the lactase gene in Scandinavian Neolithic populations, hunter-gatherers vs. farmers

Anna Linderholm1, Helena Malmström2, 5, Love Dalén3, Kerstin Lidén1, Jan Storå4, Petra Molnar4, M. Thomas P. Gilbert5, Eske Willerslev5, Gunilla Holmlund6, Anders Götherström2
1Archeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

2Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden

3Marie Curie Fellow, School of Biological Sciences, University of London, United Kingdom

4Osteoarchaeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

5Ancient DNA and Evolution Group, Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark

6National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology,Artillerigatan 12, SE-587 58 Linköping, Sweden

Genetics and culture are believed to interact, but it has been difficult to find direct evidence for the process. One example that has been put forward as a candidate is lactase persistance in adulthood, i.e. the ability to continue drinking milk. This genetic trait is believed to have evolved within a short space of time in connection with the emergence of farming cultures. Here we investigate certain Scandinavian Neolithic populations and their allele status with respect to the gene responsible for lactase persistance. We find that the allele responsible for lactase persistance was common and not significantly different from modern Swedish populations among Neolithic farmers, whereas Neolithic hunter-gatherers had a lower frequency of the allele.

aDNA analysis of human population samples from the Danish past – what have we learned?

L.C. Melchior¹, N. Lynnerup² and J.Dissing¹.

¹Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Denmark, ²Laboratory of Biological Anthropology, Institute of Forensic Medicine, University of Copenhagen, Denmark.

During an ongoing survey of the Danish genetic past we analyzed mtDNA from teeth from human remains from a range of burial sites from medieval times to the Stone Age. To ensure the highest possible degree of reliability generally accepted authentication criteria (including sequencing of multiple clones and replication by different researchers) as well as additional precautions (e.g. testing of laboratory performance) were observed.

Unequivocal assignment of mtDNA haplotypes was possible for more than 50 ancient subjects; however, the success rate varies substantially between sites. The highest success rate (11 out 11) was obtained with freshly excavated Viking Age subjects (ca AD 1,000), but good results were also obtained for recently excavated Iron Age sites (AD 0-400). Poor results were found with highly manipulated subjects (contamination) and with most of the Stone Age samples (4,500-5,000 YBP).

While laboratory related contamination can effectively be prevented by the abovementioned precautions, the most serious challenge to authenticity is caused by pre-lab contamination. This problem was tackled using several approaches including analysis of DNA damage patterns, haplotyping of archaeologists, phylogenetic testing and as the most efficient measure, sampling from the ancient subjects during exhumation. We show that reliable retrieval and analysis of DNA from ancient humans is indeed a possible undertaking.

A high degree of nucleotide diversity was observed in the ancient populations, and at four out of six locations the diversity was considerable higher than among modern Danes. Also, we observed a consistently higher abundance of Hg I (10-20%) than among modern Danes (~3%).The effect of the Black Death has been suggested as a possible explanation for a similar decline in the English genetic diversity. Interestingly, we found the highest genetic diversity in a 15^th century population sample long after the major outbreak in the14^th century.

NspI typed transition within PRNP gene (A385G / Met129Val) confirms rapid shift in allele frequencies during The Second Millennium

Henryk W. Witas1, Magdalena Kołodziejczak1, Paweł P. Liberski2
1 Dept. of Molecular Biology, Medical University of Lodz, 91-738 Lodz, Sporna 36/50, Poland

2 Dept. of Molecular Pathology and Neuropathology, Medical University of Lodz, 92-216 Łódź, Pomorska 251, Poland

Although precise biological role of prion proteins (PrPC) is still a subject of extensive study and debate, a few suggestions of their involvement in cellular processes have been described, including involvement in biology of synapse, short-term memory formation and long-term memory consolidation. Prion proteins became commonly recognizable as a cause of some human transmissible spongiform encephalopathies (TSE). Among a number of SNPs, A385G / Met129Val is assumed as a factor involved in the pathogenesis of TSEs (e.g. kuru) and a marker of memory efficiency as well. Although frequency of Met129Val alleles are precisely characterised for modern populations and its significance discussed, no data for historic and prehistoric populations to compare are available.

Specimens came from seven medieval cemeteries located throughout today’s Poland, and have been excavated recently. Teeth stored at low temperature underwent procedures generally accepted for aDNA isolation, performed automatically (MagNa Pure, Roche) at least two times on different teeth of each individual. Only the samples represented by collagen quantity above 2% dry weight, negative result of appropriate mock controls throughout isolation and amplification procedures, with successfully cloned (Amersham) and sequenced (AB 310) PCR products have been considered as authentic ancient templates. Moreover, we have applied NspI restriction analysis as a method for recognition and retrieval of undamaged ancient sequences.

The results show rapid increase in PRNP allele A frequency (Met 129) since the beginning of the Second Millennium (0.51 v. 0.65), accompanied by slight drop in heterozygotes (0.49 v. 0.39) and significant rise in Met homozygotes (0.27 v. 0.45).

As compared to present Polish as well as present European PRNP alleles frequency, medieval specimens provided the data which suggest altered mode of PRNP alleles transmission within last 35-40 generations. Although the nature of mechanism leading to observed changes is unclear, the impact of demographic factors is probably the most pronounced one affecting the process of local fluctuations of Met allele spreading out. However, the effect of selection processes should also be considered. This work is being supported by grant from Ministry of Science and Higher Education

Mice and Vikings

Eleanor Jones1
1 Department of Biology, University of York, Heslington, YO10 5DD, United Kingdom
Originally native to the northern Indian subcontinent and the Middle East, house mice (Mus musculus) have spread to their current near global distribution by exploiting a commensal niche with humans, originally in agrarian settlements. Mice also owe their current distribution pattern to human movements: they have reached the areas they now inhabit by being accidentally transported with grain and livestock foods. This close association between mice and humans means we can use information from the current genetic distribution of house mice to make inferences about past human colonisations and cultural linkages. In this study, we used mitochondrial DNA sequences from modern house mice in Great Britain, France, Ireland, Iceland, the Faeroe Islands and Norway to identify patterns in the their distribution, and tie these in to historic human migrations. The mice appear to be telling us about Norse Viking colonisations, and add a useful source of information to complement archaeological and historical data.

East Asia & Pacific

Genetic relationship of Human Skeletal Remains from an archaeological cemetery

Sang Hyun Jee 1, Yun Ji Kim 1, Yong Jae Chung1 & Min Seok Seo 1

1 Conservation Science Division, National Research Institute of Cultural Heritage, 472 Munji-dong, Yuseong-gu, Daejeon, 305-380, South Korea

We carried out genetic analyses of human skeletal remains from cemetery of a historic site, Myeong-arm-ri of Asan in South Korea. According to archaeological evidences, this site had been constructed from the Neolithic Age to the Joseon Dynasty. Twenty one human skeletons excavated from thirty pit tombs that have outer coffin build up into plaster dated to the Joseon Dynasty (14-19th century). To identify the genealogy and traditional burial pattern were assessed using mitochondrial DNA (mtDNA) and Y chromosomal STRs. We take cautious to avoid erroneous recombination by the segmental and modern contaminations were derived from researchers and all experimental stages. We sequenced the segmental amplicons of the hyper variable regions (HVRs) of mtDNA, and appointed relevant haplogroups according to the sequence polymorphism using the known mtDNA database. We also applied variable short tandem repeat (STR) marker in Y chromosome to understand paternal lineage and kinship among the burials. Especially, we interested in the four burying together and examined genetic relationship more closely between two individuals.

Not quite in the bag: A systematic bioarchaeological approach to the question of South American chickens origins

Greger Larson
1 Dept. of Archaeology, Durham University, South Road, DH1 3LE, UK

Though chickens were undoubtedly introduced into the American continents by the Spanish after their arrival in the 15th century, there is an ongoing debate as to the possible that Polynesians traveling across the Pacific introduced chickens to South America before Europeans did so. A recent publication concluded on the basis of ancient DNA extracted from an archaeological Chilean chicken bone that domestic fowl were present in a pre-Columbian context and that those chickens possessed a Polynesian genetic signature. In order to test this hypothesis, we generated mitochondrial DNA control region sequences from 41 modern, native Chilean specimens and analyzed them within a database consisting of both the published ancient DNA sequences and ~1,000 globally distributed modern domestic chicken sequences. Our modern Chilean sequences cluster closely with haplotypes predominantly distributed amongst European, Indian, and Southeast Asian chickens, consistent with a European genetic origin. The previously published, apparently pre-Columbian, Chilean specimen and seven pre-European Polynesian specimens, also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing, at this stage, no support for a Polynesian introduction of chickens to South America. Ancient DNA sequences from two archaeological sites on Easter Island, however, cluster with chickens found in Island Southeast Asia, and may represent a genetic signature of an early Polynesian dispersal as far as Easter Island. Lastly, we modeled the potential marine carbon contribution to the Chilean archaeological specimen (thus revising the derived date of the specimen) which cast doubt on the pre-Columbian age of the chicken remains. Definitive proof of a pre-Columbian introduction will require excavating more chicken bones, and further analyses of ancient DNA and radiocarbon data from Chilean and Polynesian archaeological excavations.

A New Bioarchaeological Clue for the DongHu Nationality

ZHANG Quan-chao, CHANG E，ZHU Hong

( Research Center f or Chinese Frontier A rchaeology , Jilin University , Changchun , Jilin , 130012 , China)

Abstract: DongHu nationality is a branch the Hu population who acted actively in the northeast of Yan. Whilst the remains of DongHu had not been confirmed for a long time, The tombs discovered in linxi Jinggouzi site in 2002 suggested a new clue for exploring the remains of Donghu in Chifeng area. These tombs not only meet the condionons in relation to DongHu in the aspects of time and region, but also conformed to DongHu characteristics of economic style and ethic features. In this article, human remains unearthed from the Spring and Autumn-Warring states cemetery at the Jinggouzi site in Linxi county, Inner Mongolia were studied. The morphological features of Jinggouzi group crania show that the racial type is closely related to the modern North Asiatic Mongoloids, and some physical characteristics of these skulls are closer to the ancient XianBei population in the north China and the modern Mongol. Ancient DNA sequences from ancient human remains have provided very important information on human evolution, blood relationship and migration, making ancient DNA research an important field of molecular anthropology. This study illustrates ancient DNA extraction, amplification and sequencing of five individuals of an ancient population buried in the west cemetery at Jinggouzi site in Inner Mongolia. A phylogenetic tree, a two-dimensional PC plot and MDS plot are constructed using mtDNA sequences from the ancient population and several modern Eurasian populations. However, the application of the techniques of ancient DNA allows us to explore the fasten source of the ancient population. Therefore, the genetic evidence raise the important meaning for the study of archeological culture in the east of Inner Mongolia during Spring and Autumn-Warring states. In addition, this new study which based on genetics and traditional archaeology on the development of populations from the north steppes of our country during Spring and Autumn-Warring states, provides precious data. In this study, we examine Jinggouzi population paleodiet using stable isotope ratios of carbon and nitrogen in bone collagen. Nitrogen isotope ratios of bone collagen show that Jinggouzi ancient population in primarily ate animal products with only a small amount of plant products. Carbon isotope ratios of bone collagen show that most plant products come from C₄ plant.

Physical anthropology

Obtaining population genetics data via non-destructive means: a three-dimensional analysis of human craniofacial morphology

Sabrina B. Sholts1, Sebastian Wärmländer2, & Phillip L. Walker3
1 Department of Anthropology, University of California at Santa Barbara, Department of Anthropology, University of California, Santa Barbara, CA 93106, USA

2 Division of Biophysics, Arrhenius Laboratories for Natural Science, Stockholm University, 10691 Stockholm, Sweden

3 Department of Anthropology, University of California at Santa Barbara, Department of Anthropology, University of California, Santa Barbara, CA 93106, USA

In this study, shapes extracted from the human craniofacial skeleton were used to investigate the genetic heritabilities of morphological traits. Three-dimensional point data was collected from human crania with a 3D laser scanner and used to render complete 3D surface models of the original skeletal material. 3D data analysis software was used to digitally slice the cranial models with geometric planes defined by traditional craniometric landmarks. The cross-sections produced by these planes yielded contours of cranial outlines for different craniofacial features. Using elliptical Fourier transforms, the contours were parametrized into series of Fourier coefficients, which, due to their inherent orthogonality, form suitable input parameters for statistical analysis. Principal components analysis (PCA) was employed to differentiate population groups based on shape differences in various aspects of cranio-facial skeletal morphology. This method can yield population genetics data and information on probable ancestral affinity using non-destructive analysis of human remains and with greater accuracy than with traditional craniometric studies of metric and non-metric traits. The application of this method to human skeletal collections can elucidate genetic relationships in past populations and improve our understanding of their archaeological contexts. This non-invasive method also offers a viable alternative for determining ancestral affinities between groups and individuals in cases where DNA testing is not possible, due to either the necessary destruction of bone required for DNA analysis or the degraded condition of the material.