Reassessing domestication events in the Near East: Einkorn and Triticum urartu

To reassess domestication events in the Near East, accessions of Triticum urartu from a well-described sampling were combined with a representative sample covering the Karacada? Einkorn wheat domestication. The observed DNA separation between the two wheat species accounts for the main differentiation, but geographic variation within T. urartu is evident and so is the domestication scenario among wild, feral, and domesticated Einkorn. In contrast to the clear DNA differences, it is difficult to separate living T. urartu from wild Einkorn based on morphology. With archaeobotanical material a distinction of carbonized remains of these two wheats is considered to be impossible. We reviewed the differences concerning morphology and maturity and combined these observations with information about archaeological sites in the Near East. In conclusion, the excavation sites in the middle Euphrates may contain T. urartu rather than Einkorn wheat and T. urartu may underlie the reported occurrence of the extinct 2-grained domesticated "Einkorn" wheat. The first Einkorn wheat domestication sensu stricto seems to have happened around the Karacada?, as reported earlier. The human dimension shown by the excavation of G?bekli Tepe can explain why domesticated phenotypes might have spread quickly.     

Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats’ predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor’s (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.Subject terms: Genetic variation, Molecular evolution     

Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East

The exact location of glacial refugia and the patterns of postglacial range expansion of European mammals are not yet completely elucidated. Therefore, further detailed studies covering a large part of the Western Palearctic region are still needed. In this order, we sequenced 972 bp of the mitochondrial DNA cytochrome b (mtDNA cyt b) from 124 yellow-necked fieldmice (Apodemus flavicollis) collected from 53 European localities. The aims of the study were to answer the following questions: Did the Mediterranean peninsulas act as the main refuge for yellow-necked fieldmouse or did the species also survive in more easterly refugia (the Caucasus or the southern Ural) and in Central Europe? What is the role of Turkey and Near East regions as Quaternary glacial refuges for this species and as a source for postglacial recolonisers of the Western Palearctic region? The results provide a clear picture of the impact of the quaternary glaciations on the genetic and geographic structure of the fieldmouse. This species survived the ice ages in two main refuges, the first one in the Italo-Balkan region; the second one in Turkey and the Near East regions. It is from the Balkan refuge that it recolonised all European regions at the end of the last glaciation. The Turkish and Near East populations are distinct from the European ones and they did not recolonise the Palearctic region probably because: (i) they were blocked by the Black Sea and the Caucasus, (ii) the long term presence of fieldmice populations in the Balkans prevented their expansion. These are genetically differentiated from the European and Russian ones and could be described as a particular subspecies. This result emphasises the importance of Turkey and the Near and Middle East regions as a refuge for Palearctic mammals.     

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.     

The distribution, natural habitats and availability of wild cereals in relation to their domestication in the Near East: multiple events, multiple centres

In this article we examine the natural habitats and distribution of the six wild cereals: Triticum urartu (wild urartu wheat), T. boeoticum aegilopoides (single-grained wild einkorn), T. boeoticum thaoudar (two-grained wild einkorn), T. dicoccoides (wild emmer wheat), Secale spp. (wild ryes) and Hordeum spontaneum (wild barley). A comparison of late Pleistocene/early Holocene archaeobotanical assemblages in the Near East with present-day distributions of wild cereals shows a good correlation. The regional variation in the archaeobotanical cereal assemblages and the ensuing domestication provide evidence that different cereal species were domesticated independently in different areas. Some sites were not situated near wild cereal habitats and a few were located outside the limits of distribution, even accounting for moister climatic conditions. I argue here that current models which try to explain the shift to farming have tended to over-emphasize the effect of the Younger Dryas climatic change. First, it would have had only a minor effect on cereal availability. Secondly, agriculture appears to have been established after the Younger Dryas. Thirdly, there is no evidence for a single centre of origin; agriculture arose in widely separated geographic and climatic regions. And fourthly, agriculture depends on stable climatic conditions which were not established until after the Younger Dryas.     

Non-occlusal dental microwear variability in a sample of Middle and Late Pleistocene human populations from Europe and the Near East

Non-occlusal, buccal tooth microwear variability has been studied in 68 fossil humans from Europe and the Near East. The microwear patterns observed suggest that a major shift in human dietary habits and food processing techniques might have taken place in the transition from the Middle to the Late Pleistocene populations. Differences in microwear density, average length, and orientation of striations indicate that Middle Pleistocene humans had more abrasive dietary habits than Late Pleistocene populations. Both dietary and cultural factors might be responsible for the differences observed. In addition, the Middle Paleolithic Neanderthal specimens studied show a highly heterogeneous pattern of microwear when compared to the other samples considered, which is inconsistent with a hypothesis of all Neanderthals having a strictly carnivorous diet. The high density of striations observed in the buccal surfaces of several Neanderthal teeth might be indicative of the inclusion of plant foods in their diet. The buccal microwear variability observed in the Neanderthals is compatible with an overall exploitation of both plant and meat foods on the basis of food availability. A preliminary analysis of the relationship between buccal microwear density and climatic conditions prevailing in Europe during the Late Pleistocene has been attempted. Cold climatic conditions, as indicated by oxygen isotope stage data, seem to be responsible for higher densities of microwear features, whereas warmer periods could correspond to a reduced pattern of scratch density. Such a relationship would be indicative of less abrasive dietary habits, perhaps more meat dependent, during warmer periods.     

Desert rocks as plant refugia in the Near East

The outcrops of smooth-faced rocks in Near Eastern deserts function as refugia for plants that do not fit the present local climate. They have survived in the area from periods when the continuous extensions of the moister climate enabled their penetration from the Mediterranean zone. The largest Mediterranean enclave in Near Eastern deserts and steppes is the sandstone and limestone outcrops at the upper escarpments of the southwestern Jordanian plateau, between At Tafila and Ras en Naqb, including the famous Petra and Wadi Dana. Hundreds of Mediterranean relict species and dozens of endemic species coexist with steppe and desert species in the crevices of these rocks. In this article I discuss the ecology, phytogeography, and distribution of this special habitat in Jordan, the Sinai, and Israel; and I compare the influence on past and present floras of climatic oscillations during the Pleistocene and Holocene in the Near East and Africa.     

Cross‐calibration of different radar systems for monitoring nocturnal bird migration across Europe and the Near East

Large parts of the continents are continuously scanned by terrestrial weather radars to monitor precipitation and wind conditions. These systems also monitor the mass movements of bird, bat, and insect migration, but it is still unknown how many of these systems perform with regard to detection and quantification of migration intensities of the different groups. In this study that was undertaken within five regions across Europe and the Middle East we examined to what extent bird migration intensities derived from different weather radars are comparable between each other and relate to intensities measured by local small‐scaled radars, some of them specifically developed to monitor birds. Good correspondence was found for the relative day‐to‐day pattern in migration intensities among most radar systems that were compared. Absolute intensities varied between different systems and regions. The findings of this study can be used to infer about absolute bird migration intensities measured by different radar systems and consequently help resolving methodological issues regarding the estimation of migrant numbers in the Western‐Palearctic region. It further depicts a scientific basis for the future monitoring of migratory bird populations across a large spatio‐temporal scale, predicting their movements and studying its consequences on ecological systems and human lives.     

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.     

Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa

Increasing phylogenetic resolution of the Y chromosome haplogroup tree has led to finer temporal and spatial resolution for studies of human migration. Haplogroup T, initially known as K2 and defined by mutation M70, is found at variable frequencies across West Asia, Africa, and Europe. While several SNPs were recently discovered that extended the length of the branch leading to haplogroup T, only two SNPs are known to mark internal branches of haplogroup T. This low level of phylogenetic resolution has hindered studies of the origin and dispersal of this interesting haplogroup, which is found in Near Eastern non-Jewish populations, Jewish populations from several communities, and in the patrilineage of President Thomas Jefferson. Here we map 10 new SNPs that, together with the previously known SNPs, mark 11 lineages and two large subclades (T1a and T1b) of haplogroup T. We also report a new SNP that links haplogroups T and L within the major framework of Y chromosome evolution. Estimates of the timing of the branching events within haplogroup T, along with a comprehensive geographic survey of the major T subclades, suggest that this haplogroup began to diversify in the Near East -25 kya. Our survey also points to a complex history of dispersal of this rare and informative haplogroup within the Near East and from the Near East to Europe and sub-Saharan Africa. The presence of T1a2 chromosomes in Near Eastern Jewish and non-Jewish populations may reflect early exiles between the ancient lands of Israel and Babylon. The presence of different subclades of T chromosomes in Europe may be explained by both the spread of Neolithic farmers and the later dispersal of Jews from the Near East. Finally, the moderately high frequency (-18%) of T1b* chromosomes in the Lemba of southern Africa supports the hypothesis of a Near Eastern, but not necessarily a Jewish, origin for their paternal line.     

The HLA-DRw8 lineage was generated by a deletion in the DR B region followed by first domain diversification

Sequences were generated for the first, second, and 3'UT regions of DRw8 beta-chain genes from two cell lines differing in their T cell determined allospecificities. Both have second domain sequences homologous to the B1 locus of the DRw52 family (DR3, DR5, and DRw6) and not the B3 locus. However, the 3'UT sequence is homologous to the 3'UT region of the B3 locus of the DRw52 family, and not the B1 locus. The first domain sequences are B1-like as opposed to B3-like and show polymorphism in the region encoding the putative alpha-helical region of the DR beta-chain. The easiest interpretation is that the DRw8 haplotypes constitute a sublineage within the DRw52 group and that this lineage has arisen by a small chromosomal deletion of the region between the B1 locus and the B3 locus. This deletion included the 3'UT region of the B1 locus, the B2 pseudogene, and the 5' end of the B3 locus including the exons encoding the first and second domains. After the deletion, two changes in the first domain arose by a mutational mechanism, possibly gene conversion. One of these changes parallels one seen in the DRw11 lineage.     

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome

Although crop domestication has greatly aided human civilization, the sequential domestication and regulation of most quality traits remain poorly understood. Here, we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution. The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation,whereas sugar and carotenoid contents were positively selected during domestication. Interestingly, fruit malic acid and c...     

Searching for the origins of arable weeds in the Near East

This short note adds to earlier attempts at identifying arable weeds on late Pleistocene/early Holocene sites in the Near East. Nineteen potential arable weed taxa that have no known use were selected. The occurrence of these taxa at sites with morphologically wild cereals was compared to sites with morphologically domestic cereals. The presumed arable weed taxa were as common on three PPNA (Pre Pottery Neolithic A) sites without domestication as they were on Middle PPNB (Pre Pottery Neolithic B) sites with domestication, which lends support to arguments for pre-domestic cultivation at the former sites. Arable weed taxa were less common at Natufian sites but their presence raises the question of whether they originated in cultivated fields or were the ancestors of weeds gathered accidentally alongside wild cereals in their natural habitat.     

Incongruity between Affinity Patterns Based on Mandibular and Lower Dental Dimensions following the Transition to Agriculture in the Near East,Anatolia and Europe

While it has been suggested that malocclusion is linked with urbanisation, it remains unclear as to whether its high prevalence began 8,000 years earlier concomitant with the transition to agriculture. Here we investigate the extent to which patterns of affinity (i.e., among-population distances), based on mandibular form and dental dimensions, respectively, match across Epipalaeolithic, Mesolithic, and Neolithic samples from the Near East/Anatolia and Europe. Analyses were conducted using morphological distance matrices reflecting dental and mandibular form for the same 292 individuals across 21 archaeological populations. Thereafter, statistical analyses were undertaken on four sample aggregates defined on the basis of their subsistence strategy, geography, and chronology to test for potential differences in dental and mandibular form across and within groups. Results show a clear separation based on mandibular morphology between European hunter-gatherers, European farmers, and Near Eastern transitional farmers and semi-sedentary hunter-gatherers. In contrast, the dental dimensions show no such pattern and no clear association between the position of samples and their temporal or geographic attributes. Although later farming groups have, on average, smaller teeth and mandibles, shape analyses show that the mandibles of farmers are not simply size-reduced versions of earlier hunter-gatherer mandibles. Instead, it appears that mandibular form underwent a complex series of shape changes commensurate with the transition to agriculture that are not reflected in affinity patterns based on dental dimensions. In the case of hunter-gatherers there is a correlation between inter-individual mandibular and dental distances, suggesting an equilibrium between these two closely associated morphological units. However, in the case of semi-sedentary hunter-gatherers and farming groups, no such correlation was found, suggesting that the incongruity between dental and mandibular form began with the shift towards sedentism and agricultural subsistence practices in the core region of the Near East and Anatolia.     

Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East

Background

Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East.

Methodology

Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed.

Conclusions

Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.     

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.