Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor

There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor—domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events.     

Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses

Multiple geographical regions have been proposed for the domestication of Equus caballus . It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.     

From the cradle of agriculture a handful of lentils: History of domestication

Literature on lentil domestication is reviewed, particularly considering archeobotanical, phylogenetic, and molecular evidence. Lentils are one of the oldest crops cultivated and domesticated by man. Carbonized small lentil seeds have been found in several archaeological remains starting from the Neolithic. It is probable, however, that the most ancient remains refer to wild lentils; this is difficult to ascertain since seed size was probably selected after the establishment of a domesticated lentil. It is general opinion that cultivation occurred before domestication, but for how long is still an open question. It is now well accepted that the domestication of lentils was accomplished in the Near East, in an area called “the cradle of agriculture”. The genus Lens is very small, containing only 6 taxa. A wide range of morphological and molecular evidence supports the idea that the lentil wild progenitor is Lens culinaris ssp. orientalis. On the other hand, the most distantly related species within the genus appears to be L. nigricans, whose domestication was also attempted without success. The first characters involved in lentil domestication were pod dehiscence and seed dormancy. These traits are under a simple genetic control, and therefore mutants must have been fixed in a relatively short time. These and other morphological traits possibly involved in lentil domestication have been mapped in several linkage maps. However, generally these maps are not easily integrated since they are based on a limited number of markers. Newer maps, mainly built on different kinds of molecular markers, have been more recently produced. A consensus map is needed to fill the gap in lentil breeding and, at the same time, endow with deeper information on the genetics of lentil domestication, giving new insight into the origins of this crop, which present fragmented knowledge is unable.      

Modern taurine cattle descended from small number of near-eastern founders

Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challenging process. We report mtDNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.     

Brief communication: diachronic investigation of linear enamel hypoplasia in prehistoric skeletal samples from Trentino,Italy

Linear enamel hypoplasia was scored on Neolithic, Copper Age, and Early Bronze Age samples from the Trentino region, Italy, in order to compare the extent of growth disruption in different biocultural subsistence systems (foragers with little agriculture, to agriculturists and agropastoralists). The Early Bronze Age sample shows a higher frequency of enamel defects and an earlier chronological onset than the early Neolithic sample. The higher frequency of defects in the Bronze Age sample could be linked to less diversified nutrition and, because of increased sedentism, a higher risk of disease.     

Seed dispersal in relation to the domestication of Middle East Legumes

Modification of seed dispersal was perhaps one of the most important steps towards domestication of seed crops. Among the legumes of the Middle East, four patterns of such modification can be distinguished in the process of domestication. The initial stage of domestication of lentil, pea and grass pea was apparently due to a single mutation in a major gene that prevented pod dehiscente. In chick pea the domesticated type was formed by accumulation of several mutations in minor genes that reduced the amount of pod dropping and shattering. From a seed dispersal point of view, fenugreek was preadapted to cultivation since the wild species do not shatter their seeds. In the bitter vetch and common vetch partial seed shattering apparently was tolerable and desirable under cultivation since the seed served merely for sowing the next year crop.     

How ancient DNA may help in understanding the origin and spread of agriculture

The origin and spread of agriculture have been central questions in archaeology for the last 75 years and are increasingly being addressed by a multidisciplinary approach involving biologists, ecologists, geographers and anthropologists as well as archaeologists. Molecular genetics has the potential to make an important contribution, especially by enabling the number of times that a crop or animal was domesticated to be determined. Molecular genetics can also assign approximate dates to domestication events, identify the wild progenitor of a domesticate, and provide new forms of evidence relevant to agricultural spread. With wheat, molecular genetical studies of modern plants have suggested that einkorn was domesticated just once but that emmer might have been domesticated more than once. Ancient DNA studies of animal remains have benefited from progress made with equivalent analyses of human bones, and with plant material there have been clear demonstrations of DNA preservation in desiccated seeds. Charred remains have also been shown to contain ancient DNA but this finding is unexpected in view of the high temperatures to which these seeds have supposedly been exposed. Ancient DNA studies of wheat remains have been used in taxonomic identification and in assessment of the possible bread-making quality of the wheat grown at an Early Bronze Age site in Greece.     

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs

The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare.     

Agricultural Origins: Centers and Noncenters; A Near Eastern Reappraisal

Understanding the evolutionary history of crop plants is fundamental to our understanding of their respective adaptation profiles, which in turn, is a key element in securing future yield and quality improvement. Central topics in this field concern the mono- or polyphyletic origin of crop plants, and our ability to identify the geographic location where certain crop plants have originated. Understanding the geographical pattern of domestication may also assist in reconstructing the cultural processes underlying the Neolithic (agricultural) Revolution. Here we review prevailing views on the geographic pattern of Near Eastern plant domestication, and highlight the distinction between genetic domestication events and independent cultural events. A critical evaluation of the wealth of newly published geobotanical, genetic, and archaeological data provides strong support in favor of a specific core area in southeastern Turkey where most, if not all, founder Near Eastern crops were likely domesticated.     

Population continuity, demic diffusion and Neolithic origins in central-southern Germany: The evidence from body proportions

The transition to agro-pastoralism in central Europe has been framed within a dichotomy of “regional continuity” versus exogenous “demic diffusion”. While substantial genetic support exists for a model of demographic diffusion from an ancestral source in the Near East, archaeological data furnish weak support for the “wave of advance” model. Nevertheless, archaeological evidence attests the widespread introduction of an exogenous “package” comprising ceramics, cereals, pulses and domesticated animals to central Europe at 5600 cal BCE.Body proportions are under strong climatic selection and evince remarkable stability within regional lineages. As such, they offer a viable and robust alternative to cranio-facial data in assessing hypothesised continuity and replacement with the transition to agro-pastoralism in central Europe. Humero-clavicular, brachial and crural indices in a large sample (n=75) of Linienbandkeramik (LBK), Late Neolithic and Early Bronze Age specimens from the middle Elbe-Saale-Werra valley (MESV) were compared with Eurasian and African terminal Pleistocene, European Mesolithic and geographically disparate recent human specimens.Mesolithic Europeans display considerable variation in humero-clavicular and brachial indices yet none approach the extreme “hyper-polar” morphology of LBK humans from the MESV. In contrast, Late Neolithic and Early Bronze Age peoples display elongated brachial and crural indices reminiscent of terminal Pleistocene and “tropically adapted” recent humans. These marked morphological changes likely reflect exogenous immigration during the terminal Fourth millennium cal BC. Population expansion and diffusion is a function of increased mobility and settlement dispersal concomitant with significant technological and subsistence changes in later Neolithic societies during the late fourth millennium cal BCE.     

The history of rye cultivation in Europe

During recent years finds from several prehistoric and medieval periods have thrown new light on the history of the spread of rye. It is now proven that wild rye is indigenous to Anatolia and was already domesticated there by the early Neolithic at the beginning of agriculture. Secale migrated to Central Europe as a weed among other cereals, and single grains of weed rye have been recorded there since the early Neolithic. The number of finds increased during the Bronze Age and Iron Age, and the status of rye changed from weed to crop plant, probably in the course of the early Iron Age. This acculturation of Secale cereale in central and eastern Europe was obviously independent of the earlier one in Anatolia. The first stages towards deliberate cultivation happened unintentionally through harvesting close to the ground, so that the rye was permanently represented in the seed corn. From this point rye was able to take advantage of its competitive strength on poor soils and in areas with unfavourable climate. The start of rye as a crop in its own right during the pre-Roman Iron Age and Roman period presumably took place independently in different areas. The expansion of intensive rye cultivation occurred in the Middle Ages. However, new finds from north-west Germany, which are presented here, show that in this area rye has been cultivated as a main crop on poor soils since the Roman period. In two maps all rye finds up to 1000 A.D. are shown, which after critical consideration can be regarded as cultivated rye.     

Bronze Age olive domestication in the north Jordan valley: new morphological evidence for regional complexity in early arboricultural practice from Pella in Jordan

Recent research from the site of Pella in Jordan examines the process and timing of olive cultivation. The frequent presence of olive remains from the Pottery Neolithic, beginning in the Yarmoukian, suggests that exploitation of the olive dates from as early as c. 6200 cal bce, with evidence of oil pressing from at least c. 5200 cal bce. Morphometric data, spanning the Late Neolithic to the Middle Iron Age II, using the measurement of olive endocarp length and width, demonstrates a reduction in the size variation of olive endocarps through time, in addition to an increase in their length, likely the result of selection pressure on trees. At Pella, this change occurs sometime after the Chalcolithic and before the Late Bronze Age, probably post-dating the earliest phases of the Early Bronze Age. Domestication is thus later than Teleilat Ghassul (Jordan), which has the earliest morphological evidence for olive domestication, and suggests that olive domestication was a regionally and temporally diverse process.     

Y-SNPs do not indicate hybridisation between European aurochs and domestic cattle

Background

Previous genetic studies of modern and ancient mitochondrial DNA have confirmed the Near Eastern origin of early European domestic cattle. However, these studies were not able to test whether hybridisation with male aurochs occurred post-domestication. To address this issue, Götherström and colleagues (2005) investigated the frequencies of two Y-chromosomal haplotypes in extant bulls. They found a significant influence of wild aurochs males on domestic populations thus challenging the common view on early domestication and Neolithic stock-rearing. To test their hypothesis, we applied these Y-markers on Neolithic bone specimens from various European archaeological sites.

Methods and Findings

Here, we have analysed the ancient DNA of 59 Neolithic skeletal samples. After initial molecular sexing, two segregating Y-SNPs were identified in 13 bulls. Strikingly, our results do not support the hypothesis that these markers distinguish European aurochs from domesticated cattle.

Conclusions

The model of a rapid introduction of domestic cattle into Central Europe without significant crossbreeding with local wild cattle remains unchallenged.     

Crop husbandry activities and wild plant gathering,use and consumption at the EPPNB Tell Qarassa North (south Syria)

The Early Pre-Pottery Neolithic B (EPPNB) in southwest Asia is a fundamental period in research on the origins of domesticated plants. However, there are few archaeobotanical data with which to characterise the plant-based subsistence and crop husbandry activities during this time, which hinders the understanding of the factors that triggered the appearance of plant domestication. In this paper, analyses of non-woody plant macro-remains provide new insights into subsistence activities such as crop cultivation (husbandry activities and storage) and plant use (wild plant gathering and food preparation) during the EPPNB at Tell Qarassa North (south Syria). We make comparisons between Tell Qarassa North and the evidence at earlier and later periods as to how plants were used, and highlight similarities and differences in the practices attested, as well as describing some of the consequences that these plant-related activities may have had in terms of labour and social organization during EPPNB.     

Carthamus species in the ancient Near East and south-eastern Europe: archaeobotanical evidence for their distribution and use as a source of oil

We present an overview of archaeobotanical Carthamus spp. finds from Neolithic to medieval sites in the Near East and adjacent areas. A particular focus is put on the cultivated form of the genus. Safflower appears first in a number of early Bronze Age (3000 b.c.) sites in northern and central Syria. From there it apparently spread to Egypt, the Aegean and south-eastern Europe. The Near Eastern Bronze Age evidence shows a striking exclusiveness in the distribution patterns of safflower and flax, with flax being restricted to Levantine and Iranian sites. This may reflect the contrasting ecological requirements of the two crops, with safflower being well adapted to drought and salinity and thus to arid conditions. At the same time the geographically complementary evidence may indicate a similar use of the two crops and most probably suggests that the safflower was also used for oil almost from the beginning of its cultivation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post‐medieval period and comparison with other regions in Eurasia

Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D‐loop of mitochondrial DNA (mtDNA; 213 bp) and the Y‐chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G‐oY1 of the Y‐chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations.     

Modelling the origins of legume domestication and cultivation

Ladizinsky’s (1987) mathematical model of the domestication of lentils and other Near Eastern legumes is invalid. Ladizinsky believed that the model predicts that high rates of seed harvesting would lead to fixation, in wild populations, of genes conferring lack of seed dormancy (a domesticated trait). In fact, however, the model gives rapid fixation of alleles for non-dormancy underall circumstances; gathering by humans has no effect on allelic frequencies. It appears that in these species cultivation must have preceded the morphological changes that distinguish domesticated from wild plants. The addition of more realistic assumptions to the model does not alter this conclusion. I suggest several scenarios that could explain Near Eastern legume domestication: the most plausible of these postulates that cultivation of cereals led to scheduling conflicts which necessitated the abandonment of harvesting of wild legumes, and hence the initiation of their cultivation. Mathematical modelling may be able to contribute to our understanding of agricultural origins, but it must be carried out with greater rigor and closer attention to the theoretical literature.     

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant

The location and timing of domestication of the olive tree, a key crop in Early Mediterranean societies, remain hotly debated. Here, we unravel the history of wild olives (oleasters), and then infer the primary origins of the domesticated olive. Phylogeography and Bayesian molecular dating analyses based on plastid genome profiling of 1263 oleasters and 534 cultivated genotypes reveal three main lineages of pre-Quaternary origin. Regional hotspots of plastid diversity, species distribution modelling and macrofossils support the existence of three long-term refugia; namely the Near East (including Cyprus), the Aegean area and the Strait of Gibraltar. These ancestral wild gene pools have provided the essential foundations for cultivated olive breeding. Comparison of the geographical pattern of plastid diversity between wild and cultivated olives indicates the cradle of first domestication in the northern Levant followed by dispersals across the Mediterranean basin in parallel with the expansion of civilizations and human exchanges in this part of the world.     

The oldest evidence of Nigella damascena L. (Ranunculaceae) and its possible introduction to central Europe

After the beginning of metal processing at the transition from the Neolithic to the Bronze Age, further knowledge of ore mining and smelting had spread from the Near East to central Europe. In the copper ore deposits of Schwaz, in the central part of the Alps, the oldest traces of copper mining derive from the early to middle Bronze Ages. Investigation of a middle to late Bronze Age (1410–920 cal B.C.) slag-washing site in the area revealed a carbonised seed of Nigella damascena (Ranunculaceae) (love-in-a-mist) together with individual other food plants. The plant remains had become incorporated into the slag sediments by chance and had been preserved in an excellent state due to toxic copper salts contained in the soil. Nigella damascena, like N. sativa (black cumin), is traditionally used as a condiment and healing herb in southern Europe and the Near East, but has never grown in the wild in central Europe. Until now, there has been no evidence of prehistoric large-scale cultivation of N. damascena in central Europe. This leads to two possible conclusions: the find may either originate from an exchange of goods with the cultures in the Mediterranean during the Bronze Age, or indicate an introduction of the plant by an immigrant population from that area. Implicating the latter alternative together with the archaeological context of the ore processing site suggests that Nigella damascena had been introduced to the Alps by foreign miners in the course of ore exploitation during the middle to late Bronze Age.     

Comment on "AFLP data and the origins of domesticated crops".

We review some concepts and methods of handling and using DNA fingerprinting in phylogenetic analyses related to crop domestication. Particular reference is made to AFLP markers and mode and place of einkorn, barley, and tetraploid wheat domestication in the Neolithic by human communities in the Fertile Crescent. The reconsideration of AFLP databases of domesticated and wild lines demonstrates that phylogenetic tree topologies, originally described for the three species, match closely the new results obtained by principle coordinate analyse.