Early agricultural pathways: moving outside the 'core area' hypothesis in Southwest Asia

Harvesting cereals at Tappeh Sang-e Chakhmaq and the introduction of farming in Northeastern Iran during the Neolithic

Tappeh Sang-e Chakhmaq is the only Neolithic site in Northeastern Iran, characterised by aceramic and ceramic levels corresponding to an occupation of 1500 years from the eighth to the end of the sixth millennium BCE. The Western and Eastern Mounds represent the oldest and longest occupation among the sites identified East of the Zagros, providing a unique context to explore the origin and spread of farming outside the core area of the Eastern Fertile Crescent. We present data about the first harvesting activities in the Northeastern Iranian Central Plateau by applying usewear and microtexture analysis through confocal microscopy on sickle gloss blades. Our results indicate a community of pioneer farmers who settled down in the area carrying with them both domestic cereals as well as advanced techniques of cereal cultivation. We demonstrate that most of the tools were used for harvesting cereals in a fully ripened state collected near the ground, indicating a well-established cereal cultivation strategy. The use of straight shafts with parallel inserts in Tappeh Sang-e Chakhmaq, as known in some sites in the Zagros, suggests the dispersal of farming practices and technologies from the Eastern Fertile Crescent north-eastward across Iran. We observe an evolution in the degree of ripeness of harvested cereals along the first four levels of occupation of the Western Mound, where semi-ripe harvesting is relatively important, suggesting that domestic cereals to be harvested before full maturity were introduced into the village. From the topmost of the Western Mound and along the occupation of the Eastern Mound, ripe harvesting is dominant, showing a well-established cultivation strategy of fully mature cereal. This shift could indicate an in-situ evolution towards a better-established agricultural technology, including harvesting riper crops, that would have resulted in higher yields, as cereals were collected when the grain was fully formed.

Population genomics unravels the Holocene history of bread wheat and its relatives

Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.

New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.)

Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives.

Ornamental plant domestication by aesthetics-driven human cultural niche construction

Unlike plants that were domesticated to secure food, the domestication and breeding of ornamental plants are driven by aesthetic values. Here, we examine the major elements of the extended evolutionary synthesis (EES) theory that bridges the gap between the biology of ornamental plant domestication and the sociocultural motivations behind it. We propose that it involves specific elements of cumulative cultural evolution (CCE), plant gene-human culture coevolution (PGHCC), and niche construction (NC). Moreover, ornamental plant domestication represents an aesthetics-driven dimension of human niche construction that coevolved with socioeconomic changes and the adoption of new scientific technologies. Initially functioning as symbolic and aesthetic assets, ornamental plants became globally marketed material commodities as a result of the co-dependence of human CCE and prestige-competition motivations.

Elevated CO2 modulates the effect of heat stress responses in Triticum aestivum by differential expression of isoflavone reductase-like (IRL) gene

Two wheat genotypes forming high and low biomass (HB and LB), exhibiting differential expression of an isoflavone reductase-like (IRL) gene, and resulting in contrasting grain yield under heat stress field conditions, were analyzed in detail for their responses under controlled heat and elevated CO2 conditions. Significant differences in IRL expression between the two lines were hypothesized to be the basis of their differential performance under the tested conditions and their stress tolerance potential. By a holistic approach integrating advanced cell physiological phenotyping of the antioxidative and phytohormone system in spikes and leaves with measurements of ecophysiological and agronomic traits, the genetic differences of the genotypes in IRL expression were assessed. In response to heat and elevated CO2, the two genotypes showed opposite regulation of IRL expression, which was associated with cytokinin concentration, total flavonoid contents, activity of superoxide dismutase, antioxidant capacity and photosynthetic rate in leaves and cytokinin concentration and ascorbate peroxidase activity in spikes. Our study showed that IRL expression is associated with wheat yield performance under heat stress at anthesis, mediated by diverse physiological mechanisms. Hence, based on our results, the IRL gene is a promising candidate for developing genetic markers for breeding heat-tolerant wheat.

A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.

The highly divergent Jekyll genes, required for sexual reproduction, are lineage specific for the related grass tribes Triticeae and Bromeae

Phylogenetically related groups of species contain lineage-specific genes that exhibit no sequence similarity to any genes outside the lineage. We describe here that the Jekyll gene, required for sexual reproduction, exists in two much diverged allelic variants, Jek1 and Jek3. Despite low similarity, the Jek1 and Jek3 proteins share identical signal peptides, conserved cysteine positions and direct repeats. The Jek1/Jek3 sequences are located at the same chromosomal locus and inherited in a monogenic Mendelian fashion. Jek3 has a similar expression as Jek1 and complements the Jek1 function in Jek1-deficient plants. Jek1 and Jek3 allelic variants were almost equally distributed in a collection of 485 wild and domesticated barley accessions. All domesticated barleys harboring the Jek1 allele belong to single haplotype J1-H1 indicating a genetic bottleneck during domestication. Domesticated barleys harboring the Jek3 allele consisted of three haplotypes. Jekyll-like sequences were found only in species of the closely related tribes Bromeae and Triticeae but not in other Poaceae. Non-invasive magnetic resonance imaging revealed intrinsic grain structure in Triticeae and Bromeae, associated with the Jekyll function. The emergence of Jekyll suggests its role in the separation of the Bromeae and Triticeae lineages within the Poaceae and identifies the Jekyll genes as lineage-specific.

Origins of the Apple: The Role of Megafaunal Mutualism in the Domestication of Malus and Rosaceous Trees

The apple (Malus domestica [Suckow] Borkh.) is one of the most economically and culturally significant fruits in the world today, and it is grown in all temperate zones. With over a thousand landraces recognized, the modern apple provides a unique case study for understanding plant evolution under human cultivation. Recent genomic and archaeobotanical studies have illuminated parts of the process of domestication in the Rosaceae family. Interestingly, these data seem to suggest that rosaceous arboreal crops did not follow the same pathway toward domestication as other domesticated, especially annual, plants. Unlike in cereal crops, tree domestication appears to have been rapid and driven by hybridization. Apple domestication also calls into question the concept of centers of domestication and human intentionality. Studies of arboreal domestication also illustrate the importance of fully understanding the seed dispersal processes in the wild progenitors when studying crop origins. Large fruits in Rosaceae evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene. Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers. Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning. Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).

Between domestication and civilization: the role of agriculture and arboriculture in the emergence of the first urban societies

The transition to urbanism has long focused on annual staple crops (cereals and legumes), perhaps at the expense of understanding other changes within agricultural practices that occurred between the end of the initial domestication period and urbanisation. This paper examines the domestication and role of fruit tree crops within urbanisation in both Western Asia and China, using a combination of evidence for morphological change and a database that documents both the earliest occurrence of tree fruit crops and their spread beyond their wild range. In Western Asia the domestication of perennial fruit crops likely occurs between 6500 bc and 3500 bc, although it accompanies a shift in location from that of the earliest domestications within the Fertile Crescent to Mesopotamia, where the earliest urban societies arose. For China, fruit-tree domestication dates between ca 4000 and 2500 bc, commencing after millet domestication and rice domestication in Northern and Southern China, respectively, but within the period that led up to the urban societies that characterised the Longshan period in the Yellow River basin and the Liangzhu Culture in the Lower Yangtze. These results place the domestication of major fruit trees between the end of the domestication of staple annual crops and the rise of urbanism. On this basis it is argued that arboriculture played a fundamental role within the re-organisation of existing land use, shifting the emphasis from short-term returns of cereal crops into longer term investment in the developing agricultural landscape in both Western and East Asia. In this respect perennial tree crops can be placed alongside craft specialisation, such as metallurgy and textiles, in the formation of urban centres and the shaping the organisational administration that accompanied the rise of urbanism.

Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing

Identifying the geographic origins of crops is important for the conservation and utilization of novel genetic variation. Even so, the origins of many food crops remain elusive. The tree nut crop macadamia has a remarkable domestication history, from subtropical rain forests in Australia through Hawaii to global cultivation all within the last century. The industry is based primarily on Macadamia integrifolia and M. integrifolia-M. tetraphylla hybrid cultivars with Hawaiian cultivars the main contributors to world production. Sequence data from the chloroplast genome assembled using a genome skimming strategy was used to determine population structure among remnant populations of the main progenitor species, M. integrifolia. Phylogenetic analysis of a 506 bp chloroplast SNP alignment from 64 wild and cultivated accessions identified phylogeographic structure and deep divergences between clades providing evidence for historical barriers to seed dispersal. High levels of variation were detected among wild accessions. Most Hawaiian cultivars, however, shared a single chlorotype that was also present at two wild sites at Mooloo and Mt Bauple from the northernmost distribution of the species in south-east Queensland. Our results provide evidence for a maternal genetic bottleneck during early macadamia domestication, and pinpoint the likely source of seed used to develop the Hawaiian cultivars. The extensive variability and structuring of M. integrifolia chloroplast genomic variation detected in this study suggests much unexploited genetic diversity is available for improvement of this recently domesticated crop.

The Impact of Genetic Changes during Crop Domestication

Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.

Critical role of climate change in plant selection and millet domestication in North China

While North China is one of the earliest independent centers for cereal domestication in the world, the earliest stages of the long process of agricultural origins remain unclear. While only millets were eventually domesticated in early sedentary societies there, recent archaeobotanical evidence reported here indicates that grasses from the Paniceae (including millets) and Triticeae tribes were exploited together by foraging groups from the Last Glacial Maximum to the mid-Holocene. Here we explore how and why millets were selected for domestication while Triticeae were abandoned. We document the different exploitation and cultivation trajectories of the two tribes employing ancient starch data derived from nine archaeological sites dating from 25,000 to 5500 cal BP (LGM through mid-Holocene) in North China. With this diachronic overview, we can place the trajectories into the context of paleoclimatic reconstructions for this period. Entering the Holocene, climatic changes increased the yield stability, abundance, and availability of the wild progenitors of millets, with growing conditions increasingly favoring millets while becoming more unfavorable for grasses of the Triticeae tribe. We thus hypothesize that climate change played a critical role in the selection of millet species for domestication in North China, with early domestication evidenced by 8700 cal BP.

Geographic mosaics and changing rates of cereal domestication

Domestication is the process by which plants or animals evolved to fit a human-managed environment, and it is marked by innovations in plant morphology and anatomy that are in turn correlated with new human behaviours and technologies for harvesting, storage and field preparation. Archaeobotanical evidence has revealed that domestication was a protracted process taking thousands of plant generations. Within this protracted process there were changes in the selection pressures for domestication traits as well as variation across a geographic mosaic of wild and cultivated populations. Quantitative data allow us to estimate the changing selection coefficients for the evolution of non-shattering (domestic-type seed dispersal) in Asian rice (Oryza sativa L.), barley (Hordeum vulgare L.), emmer wheat (Triticum dicoccon (Shrank) Schübl.) and einkorn wheat (Triticum monococcum L.). These data indicate that selection coefficients tended to be low, but also that there were inflection points at which selection increased considerably. For rice, selection coefficients of the order of 0.001 prior to 5500 BC shifted to greater than 0.003 between 5000 and 4500 BC, before falling again as the domestication process ended 4000-3500 BC. In barley and the two wheats selection was strongest between 8500 and 7500 BC. The slow start of domestication may indicate that initial selection began in the Pleistocene glacial era.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.

Cereal progenitors differ in stand harvest characteristics from related wild grasses

The domestication of crops in the Fertile Crescent began approximately 10,000 years ago indicating a change from a hunter-gatherer lifestyle to a sedentary, agriculture-based existence. The exploitation of wild plants changed during this transition, such that a small number of crops were domesticated from the broader range of species gathered from the wild. However, the reasons for this change are unclear.Previous studies have shown unexpectedly that crop progenitors are not consistently higher yielding than related wild grass species, when growing without competition. In this study, we replicate more closely natural competition within wild stands, using two greenhouse experiments to investigate whether cereal progenitors exhibit a greater seed yield per unit area than related wild species that were not domesticated.Stands of cereal progenitors do not provide a greater total seed yield per unit ground area than related wild species, but these crop progenitors do have greater reproductive efficiency than closely related wild species, with nearly twice the harvest index (the ratio of harvested seeds to total shoot dry mass).These differences arise because the progenitors have greater seed yield per tiller than closely related wild species, due to larger individual seed size but no reduction in seed number per tiller. The harvest characteristics of cereal progenitors may have made them a more attractive prospect than closely related wild species for the early cultivators who first planted these species, or could suggest an ecological filtering mechanism. Synthesis. Overall, we show that the maintenance of a high harvest index under competition, the packaging of seed in large tillers, and large seeds, consistently distinguish crop progenitors from closely related wild grass species. However, the archaeological significance of these findings remains unclear, since a number of more distantly related species, including wild oats, have an equally high or higher harvest index and yield than some of the progenitor species. Domestication of the earliest cereal crops from the pool of wild species available cannot therefore be explained solely by species differences in yield and harvest characteristics, and must also consider other plant traits.

Targeted resequencing reveals genomic signatures of barley domestication

Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear. To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci. We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts. These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.

Mechanisms, origin and heredity of Glu-1Ay silencing in wheat evolution and domestication

KEY MESSAGE

Allotetraploidization drives Glu-1Ay silencing in polyploid wheat. The high-molecular-weight glutenin subunit gene, Glu-1Ay, is always silenced in common wheat via elusive mechanisms. To investigate its silencing and heredity during wheat polyploidization and domestication, the Glu-1Ay gene was characterized in 1246 accessions containing diploid and polyploid wheat worldwide. Eight expressed Glu-1Ay alleles (in 71.81% accessions) and five silenced alleles with a premature termination codon (PTC) were identified in Triticum urartu; 4 expressed alleles (in 41.21% accessions), 13 alleles with PTCs and 1 allele with a WIS 2-1A retrotransposon were present in wild tetraploid wheat; and only silenced alleles with PTC or WIS 2-1A were in cultivated tetra- and hexaploid wheat. Both the PTC number and position in T. urartu Glu-1Ay alleles (one in the N-terminal region) differed from its progeny wild tetraploid wheat (1-5 PTCs mainly in the repetitive domain). The WIS 2-1A insertion occurred ~ 0.13 million years ago in wild tetraploid wheat, much later than the allotetraploidization event. The Glu-1Ay alleles with PTCs or WIS 2-1A that arose in wild tetraploid wheat were fully succeeded to cultivated tetraploid and hexaploid wheat. In addition, the Glu-1Ay gene in wild einkorn inherited to cultivated einkorn. Our data demonstrated that the silencing of Glu-1Ay in tetraploid and hexaploid wheat was attributed to the new PTCs and WIS 2-1A insertion in wild tetraploid wheat, and most silenced alleles were delivered to the cultivated tetraploid and hexaploid wheat, providing a clear evolutionary history of the Glu-1Ay gene in the wheat polyploidization and domestication processes.

On the Origin of the Non-brittle Rachis Trait of Domesticated Einkorn Wheat

Einkorn and emmer wheat together with barley were among the first cereals domesticated by humans more than 10,000 years ago, long before durum or bread wheat originated. Domesticated einkorn wheat differs from its wild progenitor in basic morphological characters such as the grain dispersal system. This study identified the Non-brittle rachis 1 (btr1) and Non-brittle rachis 2 (btr2) in einkorn as homologous to barley. Re-sequencing of the Btr1 and Btr2 in a collection of 53 lines showed that a single non-synonymous amino acid substitution (alanine to threonine) at position 119 at btr1, is responsible for the non-brittle rachis trait in domesticated einkorn. Tracing this haplotype variation back to wild einkorn samples provides further evidence that the einkorn progenitor came from the Northern Levant. We show that the geographical origin of domesticated haplotype coincides with the non-brittle domesticated barley haplotypes, which suggest the non-brittle rachis phenotypes of einkorn and barley were fixed in same geographic area in today's South-east Turkey.

Near Eastern Plant Domestication: A History of Thought

The Agricultural Revolution and plant domestication in the Near East (among its components) have fascinated generations of scholars. Here, we narrate the history of ideas underlying plant domestication research since the late 19th century. Biological and cultural perspectives are presented through two prevailing models: one views plant domestication as a protracted, unconscious evolutionary mutualistic (noncentric) process. The second advocates a punctuated, knowledge-based human initiative (centric). We scrutinize the research landscape while assessing the underlying evolutionary and cultural mechanisms. A parsimony measure indicates that the punctuated-centric view better accords with archaeological records, and the geobotany and biology of the species, and requires fewer assumptions. The protracted alternative requires many assumptions, does not account for legume biology, fails to distinguish domestication from postdomestication changes, and, therefore, is less parsimonious.

Farming legumes in the pre-pottery Neolithic: New discoveries from the site of Ahihud (Israel)

New discoveries of legumes in the lower Galilee at the prehistoric site of Ahihud in Israel shed light on early farming systems in the southern Levant. Radiocarbon dating of twelve legumes from pits and floors indicate that the farming of legumes was practiced in southern Levant as early as 10.240-10.200 (1σ) ago. The legumes were collected from pits and other domestic contexts dated to the Early Pre-Pottery Neolithic B. The legumes identified include Vicia faba L. (faba bean), V. ervilia (bitter vetch), V. narbonensis (narbon vetch), Lens sp. (lentil), Pisum sp. (pea), Lathyrus inconspicuus (inconspicuous pea) and L. hirosolymitanus (jerusalem vetchling). Comparison with coeval sites in the region show how the presence of peas, narbon vetches, inconspicuous peas, jerusalem vetchlings and bitter vetches together with faba bean and lentils is unique to the Pre-Pottery Neolithic, and might indicate specific patterns in farming or storing at the onset of agriculture.

Co-evolution of methods and thoughts in cereal domestication studies: a tale of barley (Hordeum vulgare)

Five major cereals such as wheat, rice, maize, barley and sorghum were among the first Neolithic crops that facilitated the establishment of the early agricultural societies. Since then they have remained the staple source of calories for the majority of the human population. Ample archaeological and molecular evidence has provided important insights into the domestication history of cereals but the debates on the origin of cereal crops are still far from resolved. Here, we review the recent advances in applying genome sequencing technologies for deciphering the history of cereal domestication. As a model example, we demonstrate that the evolution of thoughts on barley domestication closely followed the development of views on the rise of agriculture in the Near East in general and greatly accelerated with the advent of the genomic technologies and resources available for barley research.

Yield responses of wild C3 and C4 crop progenitors to subambient CO2 : a test for the role of CO2 limitation in the origin of agriculture

Limitation of plant productivity by the low partial pressure of atmospheric CO₂ (C_a ) experienced during the last glacial period is hypothesized to have been an important constraint on the origins of agriculture. In support of this hypothesis, previous work has shown that glacial C_a limits vegetative growth in the wild progenitors of both C₃ and C₄ founder crops. Here, we present data showing that glacial C_a also reduces grain yield in both crop types. We grew four wild progenitors of C₃ (einkorn wheat and barley) and C₄ crops (foxtail and broomcorn millets) at glacial and postglacial C_a , measuring grain yield and the morphological and physiological components contributing to these yield changes. The C₃ species showed a significant increase in unthreshed grain yield of ~50% with the glacial to postglacial increase in C_a , which matched the stimulation of photosynthesis, suggesting that increases in photosynthesis are directly translated into yield at subambient levels of C_a . Increased yield was controlled by a higher rate of tillering, leading to a larger number of tillers bearing fertile spikes, and increases in seed number and size. The C₄ species showed smaller, but significant, increases in grain yield of 10-15%, arising from larger seed numbers and sizes. Photosynthesis was enhanced by C_a in only one C₄ species and the effect diminished during development, suggesting that an indirect mechanism mediated by plant water relations could also be playing a role in the yield increase. Interestingly, the C₄ species at glacial C_a showed some evidence that photosynthetic capacity was upregulated to enhance carbon capture. Development under glacial C_a also impacted negatively on the subsequent germination and viability of seeds. These results suggest that the grain production of both C₃ and C₄ crop progenitors was limited by the atmospheric conditions of the last glacial period, with important implications for the origins of agriculture.

Early Neolithic genomes from the eastern Fertile Crescent

We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.

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.

Genetic evidence for differential selection of grain and embryo weight during wheat evolution under domestication

Wheat is one of the Neolithic founder crops domesticated ~10 500 years ago. Following the domestication episode, its evolution under domestication has resulted in various genetic modifications. Grain weight, embryo weight, and the interaction between those factors were examined among domesticated durum wheat and its direct progenitor, wild emmer wheat. Experimental data show that grain weight has increased over the course of wheat evolution without any parallel change in embryo weight, resulting in a significantly reduced (30%) embryo weight/grain weight ratio in domesticated wheat. The genetic factors associated with these modifications were further investigated using a population of recombinant inbred substitution lines that segregated for chromosome 2A. A cluster of loci affecting grain weight and shape was identified on the long arm of chromosome 2AL. Interestingly, a novel locus controlling embryo weight was mapped on chromosome 2AS, on which the wild emmer allele promotes heavier embryos and greater seedling vigour. To the best of our knowledge, this is the first report of a QTL for embryo weight in wheat. The results suggest a differential selection of grain and embryo weight during the evolution of domesticated wheat. It is argued that conscious selection by early farmers favouring larger grains and smaller embryos appears to have resulted in a significant change in endosperm weight/embryo weight ratio in the domesticated wheat. Exposing the genetic factors associated with endosperm and embryo size improves our understanding of the evolutionary dynamics of wheat under domestication and is likely to be useful for future wheat-breeding efforts.

Barley domestication: the end of a central dogma?

Genomic analysis of barley paints a picture of diffuse origins of this crop, with different regional wild populations contributing putative adaptive variations.

Barley landraces are characterized by geographically heterogeneous genomic origins

BACKGROUND

The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of multiple domestications, inconsistent with geographically circumscribed centers of origin. To better understand the genetic contributions of wild populations to domesticated barley, we compare single nucleotide polymorphism frequencies from 803 barley landraces to 277 accessions from wild populations.

RESULTS

We find that the genetic contribution of individual wild populations differs across the genome. Despite extensive human movement and admixture of barley landraces since domestication, individual landrace genomes indicate a pattern of shared ancestry with geographically proximate wild barley populations. This results in landraces with a mosaic of ancestry from multiple source populations rather than discrete centers of origin. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation in landraces of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to primitive varieties.

CONCLUSIONS

This study increases our understanding of the evolutionary process associated with the transition from wild to domesticated barley. Our findings indicate that cultivated barley is comprised of multiple source populations with unequal contributions traceable across the genome. We detect putative adaptive variants and identify the wild progenitor conferring those variants.

Barley landraces are characterized by geographically heterogeneous genomic origins

Background

The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of multiple domestications, inconsistent with geographically circumscribed centers of origin. To better understand the genetic contributions of wild populations to domesticated barley, we compare single nucleotide polymorphism frequencies from 803 barley landraces to 277 accessions from wild populations.

Results

We find that the genetic contribution of individual wild populations differs across the genome. Despite extensive human movement and admixture of barley landraces since domestication, individual landrace genomes indicate a pattern of shared ancestry with geographically proximate wild barley populations. This results in landraces with a mosaic of ancestry from multiple source populations rather than discrete centers of origin. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation in landraces of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to primitive varieties.

Conclusions

This study increases our understanding of the evolutionary process associated with the transition from wild to domesticated barley. Our findings indicate that cultivated barley is comprised of multiple source populations with unequal contributions traceable across the genome. We detect putative adaptive variants and identify the wild progenitor conferring those variants.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0712-3) contains supplementary material, which is available to authorized users.

Barley landraces are characterized by geographically heterogeneous genomic origins

BACKGROUND

The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of multiple domestications, inconsistent with geographically circumscribed centers of origin. To better understand the genetic contributions of wild populations to domesticated barley, we compare single nucleotide polymorphism frequencies from 803 barley landraces to 277 accessions from wild populations.

RESULTS

We find that the genetic contribution of individual wild populations differs across the genome. Despite extensive human movement and admixture of barley landraces since domestication, individual landrace genomes indicate a pattern of shared ancestry with geographically proximate wild barley populations. This results in landraces with a mosaic of ancestry from multiple source populations rather than discrete centers of origin. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation in landraces of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to primitive varieties.

CONCLUSIONS

This study increases our understanding of the evolutionary process associated with the transition from wild to domesticated barley. Our findings indicate that cultivated barley is comprised of multiple source populations with unequal contributions traceable across the genome. We detect putative adaptive variants and identify the wild progenitor conferring those variants.

Were Fertile Crescent crop progenitors higher yielding than other wild species that were never domesticated?

During the origin of agriculture in the Fertile Crescent, the broad spectrum of wild plant species exploited by hunter-gatherers narrowed dramatically. The mechanisms responsible for this specialization and the associated domestication of plants are intensely debated. We investigated why some species were domesticated rather than others, and which traits they shared. We tested whether the progenitors of cereal and pulse crops, grown individually, produced a higher yield and less chaff than other wild grasses and legumes, thereby maximizing the return per seed planted and minimizing processing time. We compared harvest traits of species originating from the Fertile Crescent, including those for which there is archaeological evidence of deliberate collection. Unexpectedly, wild crop progenitors in both families had neither higher grain yield nor, in grasses, less chaff, although they did have larger seeds. Moreover, small-seeded grasses actually returned a higher yield relative to the mass of seeds sown. However, cereal progenitors had threefold fewer seeds per plant, representing a major difference in how seeds are packaged on plants. These data suggest that there was no intrinsic yield advantage to adopting large-seeded progenitor species as crops. Explaining why Neolithic agriculture was founded on these species, therefore, remains an important unresolved challenge.

Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet

Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early- and late-flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation-by-distance pattern. Conversely, our data brought evidence for two well-differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.

Can Triticum urartu (Poaceae) be identified by pollen analysis? Implications for detecting the ancestor of the extinct two-grained einkorn-like wheat

The domestication of the one-grained einkorn (Triticum monococcum) in the Near East is relatively well known. However, an independent two-grained einkorn-like domestication has been archaeobotanically detected and scarce information is available. Triticum urartu, a wild wheat, was not fully described until the 1970s because the phenology does not allow it to be distinguished easily from wild einkorn (Triticum boeoticum subsp. thaoudar), although a genetic separation exists. Both species are mostly two grained and could potentially be the relatives of the extinct two-grained form. Pollen grains of several genetically well-identified wheat species, including T. urartu and T. boeoticum subsp. thaoudar, were studied by measuring the grain diameter and examining the exine sculpturing with phase-contrast microscopy and scanning electron microscopy to gain an insight into differences enabling taxonomic identification. This work showed that, although T. urartu pollen is smaller on average, grain diameter is not sufficient because of the size overlap between the species, but T. urartu presents a different exine sculpturing (scabrate) from other Triticum spp. (aerolate). This outcome is useful for taxonomists and archaeobotanists. First, it will allow a simple re-classification of herbarium materials. Second, further research could establish whether T. urartu was cultivated.

Agricultural origins from the ground up: archaeological approaches to plant domestication

The timing, geographical locations, causes, and consequences of crop domestication have long been major concerns of archaeologists, and agricultural origins and dispersals are currently more relevant than ever to scientists seeking solutions to elusive problems involving food insecurity and global health disparities. Perennial research issues that archaeologists continue to tackle include (1) thinking outside centers of origin that were based on limited and insufficient past knowledge; (2) distinguishing between single and multiple domestications of specific crops; (3) measuring the pace of domestication; and (4) decoupling domestication from agricultural economies. Paleoethnobotanists have expanded their toolkits to include analysis of ancient and modern DNA and have added increasingly sophisticated techniques in the field and the laboratory to derive precise chronological sequences to assess morphological changes in ancient and often fragmentary archaeobotanical remains and to correctly interpret taphonomy and context. Multiple lines of archaeological evidence are ideally brought together, and whenever possible, these are integrated with information from complementary sources. We discuss current perspectives and anthropological approaches to research that have as their goals the fuller and broader understanding of ancient farming societies, the plants that were domesticated, the landscapes that were created, and the culinary legacies that were passed on.

Morphological and genetic evidence for early Holocene cattle management in northeastern China

The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent ¹⁴C dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.

Agronomic conditions and crop evolution in ancient Near East agriculture

The appearance of agriculture in the Fertile Crescent propelled the development of Western civilization. Here we investigate the evolution of agronomic conditions in this region by reconstructing cereal kernel weight and using stable carbon and nitrogen isotope signatures of kernels and charcoal from a set of 11 Upper Mesopotamia archaeological sites, with chronologies spanning from the onset of agriculture to the turn of the era. We show that water availability for crops, inferred from carbon isotope discrimination (Δ(13)C), was two- to fourfold higher in the past than at present, with a maximum between 10,000 and 8,000 cal BP. Nitrogen isotope composition (δ(15)N) decreased over time, which suggests cultivation occurring under gradually less-fertile soil conditions. Domesticated cereals showed a progressive increase in kernel weight over several millennia following domestication. Our results provide a first comprehensive view of agricultural evolution in the Near East inferred directly from archaeobotanical remains.

Current perspectives and the future of domestication studies

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

Recent increases in archaeobotanical evidence offer insights into the processes of plant domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during domestication. Among domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter-gatherers whereas more often it was initiated by mobile societies of hunter-gatherers or herder-gatherers.

Evolution of crop species: genetics of domestication and diversification

Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

Did greater burial depth increase the seed size of domesticated legumes?

The independent domestication of crop plants in several regions of the world formed the basis of human civilizations, and attracts considerable interest from archaeologists and biologists. Selection under cultivation led to a suite of domestication traits which distinguish crops from their wild progenitors, including larger seeds in most seed crops. This selection may be classified as 'conscious' or 'unconscious' selection according to whether humans were aware of the changes that they were driving. The hypothesis that human cultivation buried seeds deeper than natural dispersal, exerting unconscious selection favouring larger seeds with greater reserves, was tested. Using a comparative approach, accessions of eight grain legumes, originating from independent domestication centres across several continents, were sampled. Seeds were planted at different depths in a controlled environment, and seedling emergence scored for 5 weeks after sowing. Domestication in all species was associated with increased seed mass. In three species, greater mass was not correlated with increased ability to emerge from depth. In five species, emergence depth did correlate with mass, suggesting that selection during domestication may have acted on emergence depth. However, domestication only had a significant effect in two of these species (lentil and mung bean), and the increase in depth was no more than predicted by a cube-root allometric relationship with seed mass. The results do not support the hypothesis that burial under cultivation was a general selection mechanism for increased seed mass during the domestication of grain legumes, but it may have acted in particular species or regions.

Beyond the Levant: first evidence of a pre-pottery Neolithic incursion into the Nefud Desert, Saudi Arabia

Pre-Pottery Neolithic assemblages are best known from the fertile areas of the Mediterranean Levant. The archaeological site of Jebel Qattar 101 (JQ-101), at Jubbah in the southern part of the Nefud Desert of northern Saudi Arabia, contains a large collection of stone tools, adjacent to an Early Holocene palaeolake. The stone tool assemblage contains lithic types, including El-Khiam and Helwan projectile points, which are similar to those recorded in Pre-Pottery Neolithic A and Pre-Pottery Neolithic B assemblages in the Fertile Crescent. Jebel Qattar lies ∼500 kilometres outside the previously identified geographic range of Pre-Pottery Neolithic cultures. Technological analysis of the typologically diagnostic Jebel Qattar 101 projectile points indicates a unique strategy to manufacture the final forms, thereby raising the possibility of either direct migration of Levantine groups or the acculturation of mobile communities in Arabia. The discovery of the Early Holocene site of Jebel Qattar suggests that our view of the geographic distribution and character of Pre-Pottery Neolithic cultures may be in need of revision.

On the 'lost' crops of the neolithic Near East

The claim that the 'classic' eight 'founder crop' package (einkorn wheat, emmer wheat, barley, lentil, pea, chickpea, bitter vetch, and flax) underlying the emergence of agriculture in the Near East is a relic of a larger number of domesticated species is addressed. The 'lost' crops concept relies on the idea that additional taxa were at certain points in time and in certain locations genuine crops, which were later abandoned. The issue is highly relevant to the debate concerning mono- versus polyphyletic domestication, because if there were numerous 'false starts' that were subsequently lost, this implies that plant domestication occurred over a protracted time period, and across a wide geographic range. Different criteria were used for declaring those taxa as 'lost' crops, including, but not limited to (i) identification in archaeobotanical assemblages of grains from species which are not known as crops at present; (ii) identification of such grains in what is interpreted to have been Neolithic storage facilities; and (iii) recent botanical observations on populations of crop wild relatives in disturbed habitats. The evidence for four presumed 'lost' crops (wild oat, rambling vetch, rye, and wild black lentil) and the broad bean is evaluated, and discussed in light of data on Croatian and Israeli wild pea, and Moroccan wild lentil in disturbed habitats. Based on present knowledge, the broad bean might emerge as a founder crop (without an identified wild progenitor). The same may hold true for rye, which was never lost since its adoption in the Pre-Pottery Neolithic B period in Anatolia. In the remaining three cases, there are alternative, more likely, explanations for the archaeological finds or the recent botanical observations rather than 'lost' domestication episodes.

A critical review of the protracted domestication model for Near-Eastern founder crops: linear regression, long-distance gene flow, archaeological, and archaeobotanical evidence

The recent review by Fuller et al. (2012a) in this journal is part of a series of papers maintaining that plant domestication in the Near East was a slow process lasting circa 4000 years and occurring independently in different locations across the Fertile Crescent. Their protracted domestication scenario is based entirely on linear regression derived from the percentage of domesticated plant remains at specific archaeological sites and the age of these sites themselves. This paper discusses why estimates like haldanes and darwins cannot be applied to the seven founder crops in the Near East (einkorn and emmer wheat, barley, peas, chickpeas, lentils, and bitter vetch). All of these crops are self-fertilizing plants and for this reason they do not fulfil the requirements for performing calculations of this kind. In addition, the percentage of domesticates at any site may be the result of factors other than those that affect the selection for domesticates growing in the surrounding area. These factors are unlikely to have been similar across prehistoric sites of habitation, societies, and millennia. The conclusion here is that single crop analyses are necessary rather than general reviews drawing on regression analyses based on erroneous assumptions. The fact that all seven of these founder crops are self-fertilizers should be incorporated into a comprehensive domestication scenario for the Near East, as self-fertilization naturally isolates domesticates from their wild progenitors.

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

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.

Climate change, adaptive cycles, and the persistence of foraging economies during the late Pleistocene/Holocene transition in the Levant

Climatic forcing during the Younger Dryas (∼12.9-11.5 ky B.P.) event has become the theoretical basis to explain the origins of agricultural lifestyles in the Levant by suggesting a failure of foraging societies to adjust. This explanation however, does not fit the scarcity of data for predomestication cultivation in the Natufian Period. The resilience of Younger Dryas foragers is better illustrated by a concept of adaptive cycles within a theory of adaptive change (resilience theory). Such cycles consist of four phases: release/collapse (Ω); reorganization (α), when the system restructures itself after a catastrophic stimulus through innovation and social memory--a period of greater resilience and less vulnerability; exploitation (r); and conservation (K), representing an increasingly rigid system that loses flexibility to change. The Kebarans and Late Natufians had similar responses to cold and dry conditions vs. Early Natufians and the Pre-Pottery Neolithic A responses to warm and wet climates. Kebarans and Late Natufians (α-phase) shifted to a broader-based diet and increased their mobility. Early Natufian and Pre-Pottery Neolithic A populations (r- and K-phases) had a growing investment in more narrowly focused, high-yield plant resources, but they maintained the broad range of hunted animals because of increased sedentism. These human adaptive cycles interlocked with plant and animal cycles. Forest and grassland vegetation responded to late Pleistocene and early Holocene climatic fluctuations, but prey animal cycles reflected the impact of human hunting pressure. The combination of these three adaptive cycles results in a model of human adaptation, showing potential for great sustainability of Levantine foraging systems even under adverse climatic conditions.