The effect of the Neolithic expansion on European molecular diversity

We performed extensive and realistic simulations of the colonization process of Europe by Neolithic farmers, as well as their potential admixture and competition with local Palaeolithic hunter-gatherers. We find that minute amounts of gene flow between Palaeolithic and Neolithic populations should lead to a massive Palaeolithic contribution to the current gene pool of Europeans. This large Palaeolithic contribution is not expected under the demic diffusion (DD) model, which postulates that agriculture diffused over Europe by a massive migration of individuals from the Near East. However, genetic evidence in favour of this model mainly consisted in the observation of allele frequency clines over Europe, which are shown here to be equally probable under a pure DD or a pure acculturation model. The examination of the consequence of range expansions on single nucleotide polymorphism (SNP) diversity reveals that an ascertainment bias consisting of selecting SNPs with high frequencies will promote the observation of genetic clines (which are not expected for random SNPs) and will lead to multimodal mismatch distributions. We conclude that the different patterns of molecular diversity observed for Y chromosome and mitochondrial DNA can be at least partly owing to an ascertainment bias when selecting Y chromosome SNPs for studying European populations.     

Complete mitochondrial genomes reveal neolithic expansion into Europe

The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.     

Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe

The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter-gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter-gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter-gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter-gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.     

A craniometric perspective on the transition to agriculture in Europe

Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.     

Estimating the impact of prehistoric admixture on the genome of Europeans

We inferred past admixture processes in the European population from genetic diversity at eight loci, including autosomal, mitochondrial and Y-linked polymorphisms. Admixture coefficients were estimated from multilocus data, assuming that most current populations can be regarded as the result of a hybridization process among four or less potential parental populations. Two main components are apparent in the Europeans' genome, presumably corresponding to the contributions of the first, Paleolithic Europeans, and of the early, Neolithic farmers dispersing from the Near East. In addition, only a small fraction of the European alleles seems to come from North Africa, and a fourth component reflecting gene flow from Northern Asia is largely restricted to the northeast of the continent. The estimated Near Eastern contribution decreases as one moves from east to west, in agreement with the predictions of a model in which (Neolithic) immigrants from the Near East contributed a large share of the alleles in the genome of current Europeans. Several tests suggest that probable departures from the admixture models, due to factors such as choice of the putative parental populations and more complex demographic scenarios, may have affected our main estimates only to a limited extent.     

Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations

Based on archaeological evidence, the spread of agropastoralism across Europe followed two main paths: the Danubian route, along which Neolithic farmers expanded north across the central European plains; and the Mediterranean route, where migration occurred along the coast of the Mediterranean sea. Here we examine 20 cattle breeds from the continent and assess the genetic diversity levels and relationships among the breeds using 19 microsatellite markers. Additionally, we show evidence that concords with two distinct cattle migrations from the Near East, and also demonstrate that Mediterranean cattle breeds may have had more recent input from both the Near East and Africa.     

Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process

The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter–gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter–gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter–gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter–gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter–gatherers.     

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today''s Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth–fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers.     

Genetic variation in North Africa and Eurasia: Neolithic demic diffusion vs. paleolithic colonisation

The hypothesis that both genetic and linguistic similarities among Eurasian and North African populations are due to demic diffusion of neolithic farmers is tested against a wide database of allele frequencies. Demic diffusion of farming and languages from the Near East should have determined clines in areas defined by linguistic criteria; the alternative hypothesis of cultural transmission does not predict clines. Spatial autocorrelation analysis shows significant gradients in three of the four linguistic families supposedly affected by neolithic demic diffusion; the Afroasiatic family is the exception. Many such gradients are not observed when populations are jointly analyzed, regardless of linguistic classification. This is incompatible with the hypothesis that major cultural transformations in Eurasia (diffusion of related languages and spread of agriculture) took place without major demographic changes. The model of demic diffusion seems therefore to provide a mechanism explaining coevolution of linguistic and biological traits in much of the Old World. Archaeological, linguistic, and genetic evidence agree in suggesting a multidirectional process of gene flow from the Near East in the neolithic. However, the possibility should be envisaged that some allele frequency patterns can predate the neolithic and depend on the initial spread of Homo sapiens sapiens from Africa into Eurasia. © 1994 Wiley-Liss, Inc.     

Genetics and geography of wild cereal domestication in the near east

About 12,000 years ago, humans began the transition from hunter-gathering to a sedentary, agriculture-based society. From its origins in the Near East, farming expanded throughout Europe, Asia and Africa, together with various domesticated plants and animals. Where, how and why agriculture originated is still debated. But newer findings, on the basis of genome-wide measures of genetic similarity, have traced the origins of some domesticated cereals to wild populations of naturally occurring grasses that persist in the Near East. A better understanding of the genetic differences between wild grasses and domesticated crops adds important facets to the continuing debate on the origin of Western agriculture and the societies to which it gave rise.     

Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia

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.     

A microsatellite survey of cattle from a centre of origin: the Near East

Eight humpless cattle breeds from the Near East, three from Europe, one from West Africa and two zebu breeds from India were screened with 20 microsatellite loci. Breeds from the Near East revealed considerable levels of introgression from zebu cattle, which was apparent most in populations from the East and which declined in populations further West. This nonrandom pattern is suggestive of the introduction of zebu cattle from the East. Notwithstanding the overlay of zebu alleles, it was possible to demonstrate that Near Eastern cattle exhibited significantly higher levels of allelic diversity than breeds from other regions, which is consistent with the view that this region represents a primary domestication centre for Bos taurus cattle. The hypothesis that B. taurus and B. indicus cattle have separate domestic origins is also supported by the survey, a large genetic divergence being apparent between the nonhybrid taurine and zebu groups.     

Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany

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.     

Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci

There is general agreement that the current European gene pool is mainly derived from Palaeolithic hunting-gathering and Neolithic farming ancestors, but different studies disagree on the relative weight of these contributions. We estimated admixture rates in European populations from data on 377 autosomal microsatellite loci in 235 individuals, using five different numerical methods. On average, the Near Eastern (and presumably Neolithic) contribution was between 46 and 66%, and admixture estimates showed, with all methods, a strong and significant negative correlation with distance from the Near East. If the assumptions of the model are approximately correct, i.e. if the Basques' and Near Easterners' genomes represent a good approximation to the Palaeolithic and Neolithic settlers of Europe, respectively, these results imply that half or more of the Europeans' genes are descended from Near Eastern ancestors who immigrated in Europe 10000 years ago. If these assumptions are incorrect, our results show anyway that clinal variation is the rule in the Europeans' genomes and that lower estimates of Near Eastern admixture obtained from the analysis of single markers do not reflect the patterns observed at the genomic level.     

Mitogenomes from Two Uncommon Haplogroups Mark Late Glacial/Postglacial Expansions from the Near East and Neolithic Dispersals within Europe

The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b) and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago) and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.     

Paleolithic and neolithic lineages in the European mitochondrial gene pool.

Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individuals from Europe and the Middle East distinguishes five major lineage groups with different internal diversities and divergence times. Consideration of the diversities and geographic distribution of these groups within Europe and the Middle East leads to the conclusion that ancestors of the great majority of modern, extant lineages entered Europe during the Upper Paleolithic. A further set of lineages arrived from the Middle East much later, and their age and geographic distribution within Europe correlates well with archaeological evidence for two culturally and geographically distinct Neolithic colonization events that are associated with the spread of agriculture. It follows from this interpretation that the major extant lineages throughout Europe predate the Neolithic expansion and that the spread of agriculture was a substantially indigenous development accompanied by only a relatively minor component of contemporary Middle Eastern agriculturalists. There is no evidence of any surviving Neanderthal lineages among modern Europeans.     

Modeling neolithic dispersal in central Europe: demographic implications

On the basis of new examination of ancient DNA and craniometric analyses, Neolithic dispersal in Central Europe has been recently explained as reflecting colonization or at least a major influx of near eastern farmers. Given the fact that Neolithic dispersal in Central Europe was very rapid and extended into a large area, colonization would have to be associated with high population growth and fertility rates of an expanding Neolithic population. We built three demographic models to test whether the growth and fertility rates of Neolithic farmers were high enough to allow them to colonize Central Europe without admixture with foragers. The principle of the models is based on stochastic population projections. Our results demonstrate that colonization is an unlikely explanation for the Neolithic dispersal in Central Europe, as the majority of fertility and growth rate estimates obtained in all three models are higher than levels expected in the early Neolithic population. On the basis of our models, we derived that colonization would be possible only if (1) more than 37% of women survived to mean age at childbearing, (2) Neolithic expansion in Central Europe lasted more than 150 years, and (3) the population of farmers grew in the entire settled area. These settings, however, represent very favorable demographic conditions that seem unlikely given current archaeological and demographic evidence. Therefore, our results support the view that Neolithic dispersal in Central Europe involved admixture of expanding farmers with local foragers. We estimate that the admixture contribution from foragers may have been between 55% and 72%.     

Is naked barley an eastern or a western crop? The combined evidence of archaeobotany and genetics

Forms of Hordeum vulgare ssp. vulgare (barley) that possess a naked caryopsis are an important human staple and are mainly found today in eastern Asia. However, naked barley has not always been an eastern crop: archaeobotanical data show that it was prevalent in Europe and the Near East during various periods in prehistory. In this review we have collated data on the incidence of hulled and naked barley at archaeological sites in Europe and the Near East from two sources: archaeobotanical literature reviews and an archaeobotanical database, both assembled by Helmut Kroll. We have also examined the incidence of hulled and naked barleys in extant germplasm collections. Our compilation of this archaeobotanical data has enabled us to elucidate long-term changes in the ratio of hulled to naked barley under cultivation in these regions; specifically, these records show that naked barley begins to disappear from the archaeobotanical record from the Chalcolithic/Bronze Age onwards in the Near East, and from the Iron Age/Roman periods onwards in Europe. We discuss the possible causes of this decline in naked barley cultivation in these regions, along with the present-day prevalence of naked barley landraces in eastern Asia, particularly in relation to genetic evidence, which shows that naked barley has a single origin.     

GM polymorphism and the evolutionary history of modern humans

Present human populations show a complex network of genetic relationships, which reflects mainly their unique origin and their migration and isolation history since the recent creation of modern man. The scrutiny of their genetic characteristics, according to GM polymorphism, shows that the continuity of the genetic variation between populations from neighbouring continents, assured by intermediate world part populations, is against any attempt to divide present human populations into major groups. GM polymorphism analysis also shows three remarkable levels of genetic differentiation, which would have appeared, respectively, within populations of sub-Saharan Africa, Europe and East Asia. The first small groups of people that split from the common ancestral population gave the sub-Saharan Africans. On the other hand, Asians diverged mainly from Europeans and Near East populations during a later period. The confrontation between the phylogeny and the frequency distribution of GM haplotypes shows that the ancestral population of actual South-Arabia people could be a candidate for a common ancestral population. The first major expansions of modern humans were proposed in a hypothetical scenario, which will open a new track in the research of our geographic origin.     

Genomics at the origins of agriculture,part one

The causes and consequences of the Neolithic revolution represent a fundamental problem for anthropological inquiry. Traditional archeological evidence, ethnobotanical remains, artifacts, and settlement patterns have been used to infer the transition from foraging to primary food production. Recent advances in genomics (the study of the sequence, structure, and function of the genome) has enhanced our understanding of the process of plant and animal domestication, revealed the impact that adaptation to agriculture has had on human biology, and provided clues to the pathogens and parasites thought to have emerged during the Neolithic. Genomic analysis provides insights into the complexity of the process of domestication that may not be apparent from the physical remains of bones and seeds, and allows us to measure the impact that the shift to primary food production had on the human genome. Questions related to the location and the process of domestication can be answered more fully by analyzing the genomes of the plants and animals brought under human control. The spread of the agriculture package (plants, animals, and technology) by cultural diffusion or demic expansion can also be investigated through this approach. Whether dissemination by farmers or the diffusion of farming knowledge and technology was the source of the Neolithic expansion, this process should be revealed by the patterh of genetic and linguistic diversity and language found from centers of agricultural Neolithic development. In addition, a number of pathogens that were previously thought to have been transmitted from domesticated species to human now appear to have been present in foragers long before the agricultural revolution took place. Furthermore, we now have evidence that humans were the source of the transmission of some parasites to domesticated animals. For all of these reasons, data from genomic studies are providing a more complete understanding of the origins of agriculture, a critical hallmark in human evolution.