Y chromosome genetic variation in the Italian peninsula is clinal and supports an admixture model for the Mesolithic–Neolithic encounter

Abstract

The Italian peninsula, given its geographical location in the middle of the Mediterranean basin, was involved in the process of the peopling of Europe since the very beginning, with first settlements dating to the Upper Paleolithic. Later on, the Neolithic revolution left clear evidence in the archeological record, with findings going back to 7000 B.C. We have investigated the demographic consequences of the agriculture revolution in this area by genotyping Y chromosome markers for almost 700 individuals from 12 different regions. Data analysis showed a non-random distribution of the observed genetic variation, with more than 70% of the Y chromosome diversity distributed along a North–South axis. While the Greek colonisation during classical time appears to have left no significant contribution, the results support a male demic diffusion model, even if population replacement was not complete and the degree of Neolithic admixture with Mesolithic inhabitants was different in different areas of Italy.

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Late glacial recolonization of Europe from Near Eastern refugia

 couple of quick comments on this important new paper:

• It is important to confirm the hypotheses put forward with ancient DNA data. For example, haplogroup V is said to be traced to Paleolithic SW Europe, and yet it is lacking in ancient DNA data. Looking at Jean Manco's ancient Eurasian DNA compendium, I only find a very late Neolithic hunter-gatherer sample from Pitted Ware in Sweden (2,800-2,000BC); if J/T subclades had entered Europe prior to the Neolithic, their almost complete absence in ancient DNA data is puzzling.
• Both this and the recent "Copernican" paper provide age estimates for the same nodes of the tree using the mutation rate of Soares et al. (2009). The estimaets of Pala et al. (2012) appear to be older by several thousand years than those of Behar et al. (2012) for different nodes. I don't know whether this is due to a different methodology or different dataset, but, in any case, it is a warning to avoid very close correlations between archaeological-geological events and age estimates.

UPDATE: A press release on the article.

The American Journal of Human Genetics, Volume 90, Issue 5, 915-924, 4 May 2012 doi:10.1016/j.ajhg.2012.04.003

Mitochondrial DNA Signals of Late Glacial Recolonization of Europe from Near Eastern Refugia 

Maria Pala et al. 

Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19–12 thousand years (ka) ago. 

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Horse domestication

New research indicates that domestic horses originated in the steppes of modern-day Ukraine, southwest Russia and west Kazakhstan, mixing with local wild stocks as they spread throughout Europe and Asia. The research was published today, 07 May, in the journal PNAS.

For several decades scientists puzzled over the origin of domesticated horses. Based on archaeological evidence, it had long been thought that horse domestication originated in the western part of the Eurasian Steppe (Ukraine, southwest Russia and west Kazakhstan); however, a single origin in a geographically restricted area appeared at odds with the large number of female lineages in the domestic horse gene pool, commonly thought to reflect multiple domestication "events" across a wide geographic area.

In order to solve the perplexing history of the domestic horse, scientists from the University of Cambridge used a genetic database of more than 300 horses sampled from across the Eurasian Steppe to run a number of different modelling scenarios.

Their research shows that the extinct wild ancestor of domestic horses, Equus ferus, expanded out of East Asia approximately 160,000 years ago. They were also able to demonstrate that Equus ferus was domesticated in the western Eurasian Steppe, and that herds were repeatedly restocked with wild horses as they spread across Eurasia.

ScienceNOW also covers the new research, and reports on a contrasting viewpoint: 

Not all researchers are convinced, however. Archaeologist Marsha Levine of the University of Cambridge thinks using modern genetic samples to retrace horses' evolution is a dead end. "There's been mixing of cultures and mixing of horses in this region for many thousands of years," she says. "And so when you're looking at any modern horse, you just don't know where it's from." 

Bringing together many kinds of evidence is what will ultimately answer the whens and wheres of horse domestication, Levine says. "What we need to be doing is using material from excavations, sequencing ancient genes, and combining that with what we know from archaeological evidence about how animals were used in the past."

I agree with the idea that ancient DNA will ultimately confirm/reject the model presented in the paper. Of course, it may be the case that the west Eurasian steppe was the place where horse domestication happened, but it is also the place where local horses may be descended from European, West Asian, and Central Asian breeds. I'll have to read the paper to see how the problem of possible admixture between western and eastern horse breeds on the steppe is accounted for in the paper. 

PNAS doi: 10.1073/pnas.1111122109 

Reconstructing the origin and spread of horse domestication in the Eurasian steppe 

Vera Warmuth et al. 

Despite decades of research across multiple disciplines, the early history of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and spread of horse domestication in the Eurasian steppes by fitting a spatially explicit stepping-stone model to genotype data from >300 horses sampled across northern Eurasia. We find strong evidence for an expansion of E. ferus out of eastern Eurasia about 160 kya, likely reflecting the colonization of Eurasia by this species. Our best-fitting scenario further suggests that horse domestication originated in the western part of the Eurasian steppe and that domestic herds were repeatedly restocked with local wild horses as they spread out of this area. By showing that horse domestication was initiated in the western Eurasian steppe and that the spread of domestic herds across Eurasia involved extensive introgression from the wild, the scenario of horse domestication proposed here unites evidence from archaeology, mitochondrial DNA, and Y-chromosomal DNA. 


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Agriculture arrived in Cyprus 10,600 years ago

PNAS doi: 10.1073/pnas.1201693109

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

Jean-Denis Vigne et al.

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

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 By the mid-8th millennium calBP, both sides of the Western Mediterranean were inhabited by hunter-gatherer groups which probably maintained intercontinental contacts. However, from around 7.6 ka calBP, Neolithic groups from the Eastern Mediterranean arrived in the region along the littoral of what is today Andalusia. Neolithic innovations were adopted step by step by local Epipalaeolithic groups and subsequently dispersed via already existing networks. At the same time indigenous elements were integrated into this transitional process. New ¹⁴C-data confirm the simultaneity of the Epipalaeolithic–Neolithic transition in southern Spain and northern Morocco. Results are discussed considering models and concepts from social anthropology dealing with migration and acculturation.

Technology, typology and use wear analysis of lithic tools during the early Neolithic in the cave of Murciélagos de Zuheros (Córdoba, Spain): Reflexions on the Neolithisation of the southern Iberian Peninsula

• António Faustino Carvalho^a,  , 
• Juan Francisco Gibaja^b, , 
• Beatriz Gavilán^c, 

• ^a Instituto de Arqueologia e Paleociências das Universidades Nova de Lisboa e do Algarve, Universidade do Algarve, FCHS, Campus de Gambelas, 8000-117 Faro, Portugal
• ^b Departamento de Arqueología del Consejo Superior de Investigaciones Científicas (CSIC-IMF), Investigador contratado por el Ministerio de Ciencia e Innovación - Subprograma Ramón y Cajal, C/Egipciàques, 15, 08001 Barcelona, Espagne
• ^c Universidad de Huelva, Facultad de Humanidades, Campus del El Carmen, Avda, Tres de Marzo S/N, Espagne

Abstract

The cave of Murciélagos de Zuheros (Cordoba, Spain) is one of the most important sites in Southern Iberian Peninsula. Its thick chronostratigraphic sequence includes occupations ranging from the Middle Palaeolithic to Roman times. Occupation levels corresponding to the earliest farming communities that established in modern-day Andalucia are remarkable due to its archaeological richness. This article focuses on the study of the lithic industry from these Early Neolithic levels, which is approached according to various tightly connected questions: raw material characterization, technical systems of production, and morphology and function of tools. Obtained results in their archaeological context are related to the questions on the origin of the Neolithic in Southern Iberian Peninsula.

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Emerging genetic patterns of the european neolithic

American Journal of Physical Anthropology DOI: 10.1002/ajpa.22074

Emerging genetic patterns of the european neolithic: Perspectives from a late neolithic bell beaker burial site in Germany

Esther J. Lee et al. 

Abstract 

The transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800–2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool. 


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BEAN: Bridging the European and Anatolian Neolithic

The Neolithic first appears outside its core region in the Near East and central Anatolia after 7.000 BC, in the western part of Anatolia. This is a key staging area for the further spread of the Neolithic culture through Europe. The mode and tempo of the spread of the Neolithic remains problematic: although detailed chronologies of Neolithisation exist for individual regions, a precise and comprehensive Neolithisation theory is still needed for the entire area between central Anatolia and central Europe.

Marie Curie International Training Network aims to build a new generation of students able to identify and address the main aspects of this crucial period for the future history of the entire Eurasian continent.The BEAN network focuses on demographic questions surrounding the dissemination of the cultural, technological, and biological components of the Neolithic from western Anatolia and the Balkans to the rest of Europe.  The following are the primary research questions of  Marie Curie International Training Network :

       

1.  To determine the extent to which humans migrated (along with their domesticates) into  new lands during the establishment of the Neolithic in western Anatolia and southeastern Europe.

 2.  To understand the mode and tempo of the change from foraging to farming in the Neolithic of western Anatolia and southeastern Europe and the degree of cultural exchange  between local and migrant populations.

 3.  To reconstruct the patterns of circulation of raw materials, manufactured goods and ideas.

 4. To map the population structure and estimate demographic parameters of the human  groups involved in the transition.

BEAN is a Marie Curie initial training network (ITN). The aim of the BEAN training network is to educate a new generation of researchers that will be able to combine the important aspects of  prehistoric archaeology, palaeodemography, population genetics, biostatistics, and next-generation molecular genetics while developing specialized skills in their particular scientific discipline. The broader question of the Neolithisation of Europe will serve as an intellectual framework structuring the research and training opportunities provided by BEAN network participants. 

The BEAN network proposes to carry out much-needed research into the origins of settled farming life in Europe  and the Europeans themselves while training the next generation of European researchers in the cutting-edge techniques of three different research areas:

                1.       Anthropology and Genetics

                2.       Simulations and Modelling

                3.       Prehistoric Archaeology

These  scientific disciplines reinforce each other to form a robust research framework within which researchers in the BEAN network can approach one of the most pressing archaeological questions of our time: the Neolithisation of Europe.

Simulations and Modelling

Advanced computer models can be used to simulate the diffusion of genes through a population with time, in order to test hypothetical demographic scenarios for the Neolithic transition in Western Anatolia and the Balkans.  These  models can be built using data obtained from archaeological and palaeodemographic research, and evaluated using modern and ancient DNA from populations living in the region.  By altering demographic and biological parameters, alternative hypotheses can be explored. Modelling prehistoric gene flow will enable researchers to better understand the genetic correlates and consequences of the Neolithic transition.

Anthropology and Genetics
Recent advances in the anthropological sciences have made the Neolithisation question much more tractable for modern researchers. With the advent of palaeogenetic methods such as the analysis of DNA from archaeological skeletons, and especially with the possibilities of the next generation sequencing technologies (NGS), new data have become available that now render prehistoric demographic inferences possible. When ancient DNA data are analysed by appropriate statistical inference methods, particularly those applying coalescent theory, a reliable reconstruction of past populations structure is feasible. The increasingly sophisticated methods employed by biological anthropologists to examine the morphology and composition of fossilized tissues have further enhanced the informative potential of ancient human remains.