Pre-domestication Cultivation Research Articles

Rice's trajectory from wild to domesticated in East Asia.

Rice (Oryza sativa) serves as a staple food for more than one-third of the global population. However, its journey from a wild gathered food to domestication remains enigmatic, sparking ongoing debates in the biological and anthropological fields. Here, we present evidence of rice phytoliths sampled from two archaeological sites in China, Shangshan and Hehuashan, near the lower reaches of the Yangtze River. We demonstrate the growth of wild rice at least 100,000 years before present, its initial exploitation as a gathered resource at about 24,000 years before present, its predomestication cultivation at about 13,000 years before present, and eventually its domestication at about 11,000 years before present. These developmental stages illuminate a protracted process of rice domestication in East Asia and extend the continuous records of cereal evolution beyond the Fertile Crescent.

A new functional ecological model reveals the nature of early plant management in southwest Asia.

The protracted domestication model posits that wild cereals in southwest Asia were cultivated over millennia before the appearance of domesticated cereals in the archaeological record. These 'pre-domestication cultivation' activities are widely understood as entailing annual cycles of soil tillage and sowing and are expected to select for domestic traits such as non-shattering ears. However, the reconstruction of these practices is mostly based on indirect evidence and speculation, raising the question of whether pre-domestication cultivation created arable environments that would select for domestic traits. We developed a novel functional ecological model that distinguishes arable fields from wild cereal habitats in the Levant using plant functional traits related to mechanical soil disturbance. Our results show that exploitation practices at key pre-domestication cultivation sites maintained soil disturbance conditions similar to untilled wild cereal habitats. This implies that pre-domestication cultivation did not create arable environments through regular tillage but entailed low-input exploitation practices oriented on the ecological strategies of the competitive large-seeded grasses themselves.

Harvest Techniques: Hand-Pulling and Its Potential Impact on the Archaeobotanical Record Vis a Vis Near Eastern Plant Domestication

A “cultivation prior to domestication”, or a “pre-domestication cultivation” phase features in many reconstructions of Near Eastern plant domestication. Archaeobotanists who accept this notion search for evidence to support the assumption regarding a wild plant’s cultivation phase, which in their view, preceded and eventually led to plant domestication. The presence of non-crop plant remains in the archaeobotanical record interpreted as arable weeds, i.e., weeds of cultivation, is viewed as a strong argument in support of the pre-domestication cultivation phase. Herein, we show that the simple practice of harvest by hand-pulling (uprooting) has the potential to secure an almost weed-free harvest. Indeed, rather clean (weed-free) Neolithic seed caches from a range of relevant sites were documented in archaeobotanical reports. These reports, alongside ethnographic observations suggest that (in certain cases) ancient harvest may have been carried out by selective hand-pulling. Hence, one has no reason to view archaeobotanical assemblages from occupation sites as fully representative of cultivated fields. Therefore, the concept of “arable—pre-domestication weeds”, its logic, and its potential contribution to the prevailing reconstructions of Near Eastern plant domestication need be reconsidered.

Harvesting cereals at Dja’de el-Mughara in the northern Levant: New results through microtexture analysis of Early PPNB sickle gloss (11th millennium cal BP)

The origin of cereal domestication is a key current issue of archaeological research in the Fertile Crescent. Archaeobotanical evidence highlights a complex scenario for when and where agricultural practices started. Gloss texture analysis of sickle blades with confocal microscopy represents a new contribution to the knowledge of this process. A previous study (Ibáñez et al., 2016) pointed to the Middle Euphrates in the Levant as one region where cereal cultivation occurred since the 13th millennium cal BP and progression towards cereal domestication was since then continuous, culminating in the mid-10th millennium cal BP, in the Middle PPNB. However, the transition from the Early to the Middle PPNB – between 10,200–9,800 cal BP –, a key period previous to the appearance of the first domestic cereals, is not fully understood. This paper presents the quantitative analysis of gloss microtexture on 48 sickles blades from the Early PPNB levels of Dja’de el-Mughara (c. 10,650–10,350 cal BP), where pre-domestic cultivation of wild cereals is attested by archaeobotanical studies. Gloss texture analysis of sickle blades indicates that though reaping semi-ripe cereals associated to cutting wild cultivated cereals is dominant, other group of tools reaped cereals in an advanced degree of maturity. Tools used for cutting green cereals are also present, suggesting that wild cereals in natural stands were also exploited. This study exhibits the complexity of the cereal harvesting strategies at this transitional period, suggesting the exploitation of cereal populations that were in different phases of the domestication process. The results were then compared with the previous research about 50 sickle elements from several sites from the Late Natufian (13th millennium cal BP) to the Late PPNB (late 10th millennium cal BP) in the Middle Euphrates.

La explotación de las plantas y los inicios de la agricultura en el Próximo Oriente: 20 años de investigación arqueobotánica

This paper deals with the development of Near Eastern archaeobotany during the past two decades. It focuses on the advances of the discipline, particularly on the progress made in pre-agrarian plant use and the origins of agriculture. The main Palaeolithic and Epipalaeolithic sites where plant use has been well attested are discussed while issues such as pre-domestic cultivation and plant domestication are also analyzed.

Phytolith assemblage analysis for the identification of rice paddy

The rice arable system is of importance to both society and the environment. The emergence of rice paddies was a crucial step in the transition from pre-domestic cultivation to systematic land use and management. However, many aspects of the formation of rice farming systems remain unclear. An important reason is the lack of reliable methods for identifying early rice paddies. One possible means of remedying this knowledge deficit is through analysis of phytolith assemblages, which are closely related to their parent plant communities. In this study, phytolith assemblages from 27 surface soil samples from wild rice fields, 91 surface soil samples from modern rice paddies, and 50 soil samples from non-rice fields were analysed to establish a discriminant function. This discriminant function enabled classification of 89.3% of the samples into appropriate groups. Further, the results suggested that phytolith assemblages can be used to identify rice fields and differentiate between wild rice fields and domesticated rice fields. The method was demonstrated to be an effective way of utilising the large amounts of unidentifiable phytoliths discovered at archaeological sites to provide a modern analogue that may be a valuable key to unlocking the past.

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.

A systematic review of wild grass exploitation in relation to emerging cereal cultivation throughout the Epipalaeolithic and aceramic Neolithic of the Fertile Crescent

The present study investigates the occurrence of wild grasses at Epipalaeolithic and aceramic Neolithic sites in the Near East in order to assess their role in subsistence economies alongside the emergence of cereal cultivation. We use Chogha Golan in the foothills of the central Zagros Mountains (ca. 11.7–9.6 ka cal. BP) as a case study, where the archaeobotanical data suggest the frequent exploitation of a complex of wild grasses for almost 2,000 years. Domesticated emmer replaced these wild grasses as the major food resources towards the end of occupation at the site (ca. 9.8 ka cal. BP). We discuss possible implications of this development and conclude that the traditional concept of pre-domestication cultivation seems unsuited for explaining the patterns from Chogha Golan. These data are in good accordance with the overall picture in the Zagros Mountains, where wild grasses were routinely gathered throughout the early Holocene. In contrast, wild grasses were gradually replaced by wild cereals in the Levantine corridor since the end of the Pleistocene. However, several sites located in this region provide evidence for a continuous exploitation of wild grasses alongside emerging cereal cultivation and most of these taxa were part of the earliest segetal floras that evolved with the appearance of domestic cereals throughout the 11th millennium cal. BP. Some sites contemporary to the Pre-Pottery Neolithic B still provide evidence for the usage of wild grasses, which possibly reflects the utilization of edible arable weeds and continuous gathering of wild grasses by more mobile groups.

New insights on plant domestication, production intensification, and food storage: the archaeobotanical evidence from PPNA Dhra‘

We present detailed accounts of the archaeobotanical remains recovered from the excavations of the southern Levantine Pre-Pottery Neolithic A site of Dhra‘, including metric and morphological analysis of barley grains. Comparisons with other early Epi-Palaeolithic and Neolithic sites indicate that the Dhra‘ grains are larger than recorded wild specimens, but fall at the lower range of domestic species, consistent with intermediary pre-domestication cultivation status. We contextualize these results in relation to associated evidence for food storage at Dhra‘, as well as the ecology of wild plants and early crops, and processing technologies across the Levant.

Usewear and residue analyses of experimental harvesting stone tools for archaeological research

Chinese millets (Setaria italica and Panicum miliaceum), first domesticated in north China, were among the most important East Asian crops in the past. Previous studies have mainly focused on the morphological changes of millet grains for evidence of domesticity, but very few attempts have been made to understand the predomestication cultivation processes that predated morphological domestication and were likely involved with using certain harvesting methods. In order to develop methods for detecting evidence of this early stage of domestication we conducted a series of experiments cutting various wild and domesticated plants with stone tools, and analyzed the usewear traces and starch and phytolith residues on these tools. To evaluate the origins of the tool residues, we also extracted microbotanical contents from the stems and leaves of related plants with a focus on starch, and observed in-situ starches in leaves. The results show that stone tools with varying hardness and surface roughness used for harvesting cereals show diverse forms of polish and striations on their edges, and the confirmation of relatively large non-transient starch grains existing in stems/leaves provides a new opportunity for functional analysis of archaeological tools. This study proposes a multi-proxy approach to examine cutting tools for the evidence of cereal harvesting, particularly millets.

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.

Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture in the Near East

This paper debates claims that plant domestication occurred rapidly in a single restricted sub-section of the Near Eastern Fertile Crescent. Instead we argue for numerous parallel processes of domestication across the region in the Early Holocene. While a previous generation of genetic results seemed to support a single ‘core area’, the accumulation of genetic evidence and refinements in methods undermine this, pointing increasingly towards multiple geographical origins. We stress that it is important to recognize that modern germplasm collections are an imperfect sample of the diversity of wild and cultivated populations of the past, which included some extinct lineages. We briefly synthesize the accumulated data from archaeobotany, defending the reliability of archaeological science to inform us about the past plant populations used by people. These data indicate an extended period of pre-domestication cultivation of at least a millennium and the slow evolution of morphological domestication adaptations in crop plants. The appearance of early cultivars and domesticates was spread piecemeal around the Near East, and a whole crop package is not evident. The ‘core area’ claimed by some authors has no better claim for primacy or completeness in comparison to other parts of the Near East. Evidence from zooarchaeology similarly points towards a diffuse appearance of various domesticated animals. The ‘non-centric’ appearance of domesticates from the Near East is therefore similar to the emerging evidence from many other regions of the world where plants were domesticated. We develop a hypothesis of why this should be expected given that anatomically modern human ancestors shared practices of vegetation management and planting, the necessary background knowledge for cultivation. Cultivation then was not a rare discovery but was a strategic and systematic shift in economies. The question then becomes why it was developed in the particular regions and periods where it appeared.

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.

A simulation of the effect of inbreeding on crop domestication genetics with comments on the integration of archaeobotany and genetics: a reply to Honne and Heun

Archaeobotanical evidence for Near Eastern einkorn wheat, barley, and Chinese rice suggests that the fixation of key domestication traits such as non-shattering was slower than has often been assumed. This suggests a protracted period of pre-domestication cultivation, and therefore implies that both in time and in space the initial start of cultivation was separated from eventual domestication, when domesticated and wild populations would have become distinct gene pools. Archaeobotanical evidence increasingly suggests more pathways to cultivation than are represented by modern domesticated crop lines, including apparent early experiments with cultivation that did not lead to domestication, and early domesticates, such as two-grained einkorn and striate-emmeroid wheats, which went extinct in prehistory. This diverse range of early crops is hard to accommodate within a single centre of origin for all early Near Eastern cultivars, despite suggestions from genetic datasets that single origins from a single centre ought to be expected. This apparent discrepancy between archaeobotany and genetics highlights the need for modelling the expected genetic signature of different domestication scenarios, including multiple origins. A computer simulation of simple plant populations with 20 chromosomes was designed to explore potential differences between single and double origins of domesticated populations as they might appear in genomic datasets millennia later. Here we report a new simulation of a self-pollinating (2% outbreeding) plant compared to panmictic populations, and find that the general outcome is similar with multiple starts of cultivation drifting towards apparent monophyly in genome-wide phylogenetic analysis over hundreds of generations. This suggests that multiple origins of cultivation of a given species may be missed in some forms of modern genetic analysis, and it highlights the need for more complex modelling of population genetic processes associated with the origins of agriculture.

Late Pleistocene and early Holocene climate and the beginnings of cultivation in northern Syria

Climate change has been interpreted as a contributing factor to the emergence of agriculture in the Near East. We examine how climate change may have affected the availability of food plants and their cultivation in northern Syria at the end of the Pleistocene and the beginning of the Holocene. Charred plant remains from sites representing 11 archaeological levels indicate that during the late Pleistocene rye was commonly used, together with seeds gathered from the floodplain. During the early Holocene, rye and floodplain plants go out of use and barley then emmer wheat become common, pulses, lentils, peas and vetches increase in use and figs, chickpeas and horse beans were introduced. Pre-domestic cultivation is difficult to identify in the absence of morphologically domesticated plants. We cannot identify precisely when cultivation started but the possibility of cultivation is not excluded for the late Pleistocene, however we argue that it did not become a reliable means of subsistence until the Holocene. This period coincides with a decrease in the amplitude of climatic oscillations and global warming. With these conditions, combined with an increase in rainfall, we suggest cultivation developed into a sustainable economy. The earliest morphologically domestic cereals found in this area date to about 10 000 cal. yr BP. These may have been slow to become established because seed for sowing may have occasionally been replenished from the wild.

The genetic expectations of a protracted model for the origins of domesticated crops

Until recently, domestication has been interpreted as a rapid process with little predomestication cultivation and a relatively rapid rise of the domestication syndrome. This interpretation has had a profound effect on the biological framework within which investigations into crop origins have been carried out. A major underlying assumption has been that artificial selection pressures were substantially stronger than natural selection pressures, resulting in genetic patterns of diversity that reflect genetic independence of geographic localities. Recent archaeobotanical evidence has overturned the notion of a rapid transition, resulting in a protracted model that undermines these assumptions. Conclusions of genome-wide multilocus studies remain problematic in their support of a rapid-transition model by indicating that domesticated crops appear to be associated by monophyly with only a single geographic locality. Simulations presented here resolve this conflict, indicating that the results observed in such studies are inevitable over time at a rate that is largely influenced by the long-term population size. Counterintuitively, multiple origin crops are shown to be more likely to produce monophyletic clades than crops of a single origin. Under the protracted transition, the importance of the rise of the domestication syndrome becomes paramount in producing the patterns of genetic diversity from which crop origins may be deduced. We identify four different interacting levels of organization that now need to be considered to track crop origins from modern genetic diversity, making crop origins a problem that could be addressed through system-based approaches.

Serendipitous backyard hybridization and the origin of crops

Backyard gardens, dump heaps, and kitchen middens are thought to have provided important venues for early crop domestication via generation of hybrids between otherwise isolated plant species. However, this process has rarely been demonstrated empirically. For the majority of polyploid crops, it remains uncertain to what extent hybridization and polyploidization preceded domestication or were precipitated by human activities. Using archaeological, ethnobotanical, geographical, and genetic data, we investigate the extent and significance of predomestication cultivation, backyard sympatry, and spontaneous hybridization for the Mimosoid legume tree Leucaena, which is used as a food crop throughout south-central Mexico. We show that predomestication cultivation was widespread, involved numerous independent transitions from the wild to cultivation, and resulted in extensive artificial sympatry of 2-6 species locally and 13 species in total. Using chloroplast and rapidly evolving nuclear-encoded DNA sequences, we demonstrate that hybridization in Leucaena has been extensive and complex, spawning a diverse set of novel hybrids as a result of juxtaposition of species in cultivation. The scale and complexity of hybridization in Leucaena is significantly greater than that documented for any other Mexican plant domesticates so far. However, there are striking parallels between Leucaena and the other major Mexican perennial domesticates Agave and Opuntia, which show very similar domestication via backyard hybridization pathways. Our results suggest that backyard hybridization has played a central role in Mesoamerican crop domestication and demonstrate that the simple step of bringing species together in cultivation can provide a potent trigger for domestication.

Presumed domestication? Evidence for wild rice cultivation and domestication in the fifth millennium BC of the Lower Yangtze region

Prompted by a recent article by Jiang and Liu in Antiquity (80, 2006), Dorian Fuller and his co-authors return to the question of rice cultivation and consider some of the difficulties involved in identifying the transition from wild to domesticated rice. Using data from Eastern China, they propose that, at least for the Lower Yangtze region, the advent of rice domestication around 4000 BC was preceded by a phase of pre-domestication cultivation that began around 5000 BC. This rice, together with other subsistence foods like nuts, acorns and waterchestnuts, was gathered by sedentary hunter-gatherer-foragers. The implications for sedentism and the spread of agriculture as a long term process are discussed.

From the PPNA to the PPNB : new views from the Southern Levant after excavations at Zahrat adh-Dhra' 2 in Jordan

Results from excavations at the Pre-Pottery Neolithic A (PPNA) site of Zahrat adh-Dhra' 2 (ZAD 2) in Jordan promise to resolve ambiguity over the introduction of the Pre-Pottery Neolithic В (PPNB) period in the southern Levant. Zahrat adh-Dhra ' 2 is the first southern PPNA site to date exclusively to the late PPNA period (9 600-9 300 BP/ 9 200-8 300 cal ВС). The settlement is a small mound containing a single phase of curvilinear architecture. It has yielded a range of characteristic PPNA material culture items and practices, including evidence of cranial removal, a varied ground stone industry with cup-hole mortars, geometrically incised plaques and pebbles ; and a lithic assemblage which includes bladelet cores, a preponderance of bladelets, borers, Beit Та 'amir sickles, Hagdud truncations, picks, edge-ground axes, and tranchet axes. It lacks typical PPNB features such as naviform blade core technology, and notched and tanged projectile points. It also bears evidence for a subsistence economy based on hunting, gathering and the cultivation of cereals and possibly legumes (so-called "pre-domestication cultivation"). ZAD 2 casts doubt upon the authenticity of a prominent chronological scheme which places the southern Levantine Early PPNB phase dating from (9 600-9 200 BP/ also 9 200-8 300 cal ВС). Details of the radiocarbon dates obtained for ZAD 2 and their relationship to the stratigraphie order of the site are given here. Nevertheless, a marked plateau on the early Holocene part of the radiocarbon calibration curve renders it difficult to sequentially order calibrated dates within the 9 600-9 200 BP period, and thus to distinguish between the alternative chronological schemes. In the future, Bayesian modeling of date sequences from individual sequences may assist in this regard. Bayesian modeling of the ZAD 2 dates was undertaken here in order to estimate a likely occupational span for the site. This analysis suggests that the occupation of ZAD 2 can be constrained to the period 8 800-8 450 cal ВС. Yet more recently discovered than ZAD 2, a new phase at the site of'Motza in Israel promises to further elucidate the question of the EPPNB in the southern Levant. With these fresh perspectives newly at hand, we review evidence from several southern Levantine sites previously claimed as exemplars of the southern EPPNB. We also examine their relation to Syrian Pre-Pottery Neolithic sites ; in particular Dja 'de al-Mughara and the new work at Tell Aswad in the Damascus Basin which has radically altered our understanding of that site and weakened its pivotal importance as a reference point for the southern Levantine PPNA and EPPNB. We conclude that, according to the debate as it has been played out in the uncalibrated chronology, the EPPNB phase originated in north Syria around 9 600 BP and the southern Levantine PPNB began around 9 350/9 300 BP.