Grazing animals drove domestication of grain crops

The sleeping crops of eastern North America: a new synthesis

Indigenous peoples in eastern North America domesticated a diverse group of annual crops. Several of these crops fell out of cultivation around the time of European colonization, and their domesticated forms are known only from the archaeological record. These crops have previously been characterized as lost, but in the context of a renaissance in Indigenous agriculture in this region, they are perhaps better understood as sleeping: this ancient agricultural system and its myriad ecosystem interactions could be reawakened. I briefly review the history of research on native eastern North American crops, and then synthesize recent research in terms of three themes: new models of domestication based on ecological, experimental and archaeological studies; new insights into the evolution of ancient agrobiodiversity; and an increasingly expansive understanding of the domesticated landscapes of ancient eastern North America. I conclude by suggesting some priorities for future research, and considering this sleeping agricultural system as a source of alternative crops and methods for the North American midcontinent in an era of rapid climate change.This article is part of the theme issue 'Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future'.

Early evidence of avocado domestication from El Gigante Rockshelter, Honduras

Molecular research suggests that avocados (Persea americana Mill.) were domesticated multiple times in the Americas. Seed exchange, hybridization, and cloning have played an essential role across their wild distribution from Mexico to South America to create the modern varieties of today. Archaeological sites with well-preserved and directly radiocarbon-dated botanical assemblages are rare, however, so we know very little about the complexities of the domestication process. Here, we define an early locus of avocado domestication using well-dated desiccated and carbonized avocado remains from El Gigante rockshelter in western Honduras spanning the last 11,000 y. Measurements of avocado seeds and rinds show evidence for long-term management resulting in selection for larger, more robust fruits through time that culminated by 2,250 to 2,080 calendar B.P. (cal. B.P.). However, human-directed selection for larger fruits with thicker rinds is evident as early as 7,565 to 7,265 cal. B.P. Seed morphology is similar to P. americana var. guatemalensis and is congruent with genetic data for the development of this variety in both the highlands of Guatemala and Honduras. Increases in seed size and rind thickness through time are consistent with genetic evidence for the enrichment of putative candidate genes for fruit development and ripening in this variety.

Domestication as the evolution of interspecies cooperative breeding

We propose that domestication is the result of interspecies cooperative breeding. Considering domestication as an outcome of cooperative breeding can explain how domestication occurs in both plants and animals, encompass cases of domestication that do not involve humans, and shed light on why humans are involved in so many domesticatory relationships. We review the cooperative breeding model of human evolution, which posits that care of human infants by alloparents enabled the evolution of costly human brains and long juvenile development, while selecting for tolerance of strangers. We then explore how human cooperation in the protection and provisioning of young plants and animals can explain the evolution of domestication traits such as changes in development; loss of aggressive, defensive, and bet-hedging aspects of the phenotype; and increased fertility. We argue that the importance of cooperative breeding to human societies has made humans especially likely to enter into interspecies cooperative breeding relationships.

Evolutionary pathways to lower biomass allocation to the seed coat in crops: insights from allometric scaling

Crops generally have seeds larger than their wild progenitors´ and with reduced dormancy. In wild plants, seed mass and allocation to the seed coat (a proxy for physical dormancy) scale allometrically so that larger seeds tend to allocate less to the coats. Larger seeds and lightweight coats might thus have evolved as correlated traits in crops. We tested whether 34 crops and 22 of their wild progenitors fit the allometry described in the literature, which would indicate co-selection of both traits during crop evolution. Deviations from the allometry would suggest that other evolutionary processes contribute to explain the emergence of larger, lightweight-coated seeds in crops. Crops fitted the scaling slope but deviated from its intercept in a consistent way: Seed coats of crops were lighter than expected by their seed size. The wild progenitors of crops displayed the same trend, indicating that deviations cannot be solely attributed to artificial selection during or after domestication. The evolution of seeds with small coats in crops likely resulted from a combination of various pressures, including the selection of wild progenitors with coats smaller than other wild plants, further decreases during early evolution under cultivation, and indirect selection due to the seed coat-seed size allometry.

Archaeobotanical evidence supports indigenous cucurbit long-term use in the Mesoamerican Neotropics

The squash family (Cucurbitaceae) contains some of the most important crops cultivated worldwide and has played an important ecological, economic, and cultural role for millennia. In the American tropics, squashes were among the first cultivated crop species, but little is known about how their domestication unfolded. Here, we employ direct radiocarbon dating and morphological analyses of desiccated cucurbit seeds, rinds, and stems from El Gigante Rockshelter in Honduras to reconstruct human practices of selection and cultivation of Lagenaria siceraria, Cucurbita pepo, and Cucurbita moschata. Direct radiocarbon dating indicates that humans started using Lagenaria and wild Cucurbita starting ~ 10,950 calendar years before present (cal B.P.), primarily as watertight vessels and possibly as cooking and drinking containers. A rind directly dated to 11,150-10,765 cal B.P. represents the oldest known bottle gourd in the Americas. Domesticated C. moschata subsequently appeared ~ 4035 cal B.P., followed by domesticated C. pepo ~ 2190 cal B.P. associated with increasing evidence for their use as food crops. Multivariate statistical analysis of seed size and shape show that the archaeological C. pepo assemblage exhibits significant variability, representing at least three varieties: one similar to present-day zucchini, another like present-day vegetable marrow, and a native cultivar without modern analogs. Our archaeobotanical data supports the hypothesis that Indigenous cucurbit use started in the Early Holocene, and that agricultural complexity during the Late Holocene involved selective breeding that encouraged crop diversification.

Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes

Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.

Trans-Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras

El Gigante rockshelter in western Honduras provides a deeply stratified archaeological record of human-environment interaction spanning the entirety of the Holocene. Botanical materials are remarkably well preserved and include important tree (e.g., ciruela (Spondias), avocado (Persea americana)) and field (maize (Zea mays), beans (Phaseolus), and squash (Cucurbita)) crops. Here we provide a major update to the chronology of tree and field crop use evident in the sequence. We report 375 radiocarbon dates, a majority of which are for short-lived botanical macrofossils (e.g., maize cobs, avocado seeds, or rinds). Radiocarbon dates were used in combination with stratigraphic details to establish a Bayesian chronology for ~9,800 identified botanical samples spanning the last 11,000 years. We estimate that at least 16 discrete intervals of use occurred during this time, separated by gaps of ~100-2,000 years. The longest hiatus in rockshelter occupation was between ~6,400 and 4,400 years ago and the deposition of botanical remains peaked at ~2,000 calendar years before present (cal BP). Tree fruits and squash appeared early in the occupational sequence (~11,000 cal BP) with most other field crops appearing later in time (e.g., maize at ~4,400 cal BP; beans at ~2,200 cal BP). The early focus on tree fruits and squash is consistent with early coevolutionary partnering with humans as seed dispersers in the wake of megafaunal extinction in Mesoamerica. Tree crops predominated through much of the Holocene, and there was an overall shift to field crops after 4,000 cal BP that was largely driven by increased reliance on maize farming.

Prehistoric Plant Exploitation and Domestication: An Inspiration for the Science of De Novo Domestication in Present Times

De novo domestication is a novel trend in plant genetics, where traits of wild or semi-wild species are changed by the use of modern precision breeding techniques so that they conform to modern cultivation. Out of more than 300,000 wild plant species, only a few were fully domesticated by humans in prehistory. Moreover, out of these few domesticated species, less than 10 species dominate world agricultural production by more than 80% today. Much of this limited diversity of crop exploitation by modern humans was defined early in prehistory at the emergence of sedentary agro-pastoral cultures that limited the number of crops evolving a favorable domestication syndrome. However, modern plant genetics have revealed the roadmaps of genetic changes that led to these domestication traits. Based on such observations, plant scientists are now taking steps towards using modern breeding technologies to explore the potential of de novo domestication of plant species that were neglected in the past. We suggest here that in this process of de novo domestication, the study of Late Paleolithic/Late Archaic and Early Neolithic/Early Formative exploration of wild plants and identification of neglected species can help identify the barriers towards domestication. Modern breeding technologies may then assist us to break these barriers in order to perform de novo domestication to increase the crop species diversity of modern agriculture.

Plant domestication and agricultural ecologies

Plant life defines the environments to which animals adapt and provides the basis of food webs. This was equally true for hunter-gatherer economies of ancestral humans, yet through the domestication of plants and the creation of agricultural ecologies based around them, human societies transformed vegetation and transported plant taxa into new geographical regions. These human-plant interactions ultimately co-evolved, increasing human population densities, technologies of farming, and the diversification of landraces and crop complexes. Research in archaeology on preserved plant remains (archaeobotany) and on the genomes of crops, including ancient genomes, has transformed our scientific understanding of the complex relationships between humans and plants that are entailed by domestication. Key realizations of recent research include the recognition that: the co-evolution of domesticates and cultures was protracted, the adaptations of plant populations were unintended results of human economies rather than intentional breeding, domestication took place in dozens of world regions involving different crops and cultures, and convergent evolution can be recognized among cropping types - such as among seed crops, tuber crops, and fruit trees. Seven general domestication pathways can be defined for plants. Lessons for the present-day include: the importance of diversity in the past; genetic diversity within species has the potential to erode over time, but also to be rescued through processes of integration; similarly, diversification within agricultural ecosystems has undergone processes of decline, including marginalised, lost and 'forgotten' crops, as well as processes of renewal resulting from trade and human mobility that brought varied crops and varieties together.

Bearing Fruit: Miocene Apes and Rosaceous Fruit Evolution

Extinct megafaunal mammals in the Americas are often linked to seed-dispersal mutualisms with large-fruiting tree species, but large-fruiting species in Europe and Asia have received far less attention. Several species of arboreal Maloideae (apples and pears) and Prunoideae (plums and peaches) evolved large fruits starting around nine million years ago, primarily in Eurasia. As evolutionary adaptations for seed dispersal by animals, the size, high sugar content, and bright colorful visual displays of ripeness suggest that mutualism with megafaunal mammals facilitated the evolutionary change. There has been little discussion as to which animals were likely candidate(s) on the late Miocene landscape of Eurasia. We argue that several possible dispersers could have consumed the large fruits, with endozoochoric dispersal usually relying on guilds of species. During the Pleistocene and Holocene, the dispersal guild likely included ursids, equids, and elephantids. During the late Miocene, large primates were likely also among the members of this guild, and the potential of a long-held mutualism between the ape and apple clades merits further discussion. If primates were a driving factor in the evolution of this large-fruit seed-dispersal system, it would represent an example of seed-dispersal-based mutualism with hominids millions of years prior to crop domestication or the development of cultural practices, such as farming.

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.

Pathways to de novo domestication of crop wild relatives

Growing knowledge about crop domestication, combined with increasingly powerful gene-editing toolkits, sets the stage for the continual domestication of crop wild relatives and other lesser-known plant species.

Exaptation Traits for Megafaunal Mutualisms as a Factor in Plant Domestication

Megafaunal extinctions are recurring events that cause evolutionary ripples, as cascades of secondary extinctions and shifting selective pressures reshape ecosystems. Megafaunal browsers and grazers are major ecosystem engineers, they: keep woody vegetation suppressed; are nitrogen cyclers; and serve as seed dispersers. Most angiosperms possess sets of physiological traits that allow for the fixation of mutualisms with megafauna; some of these traits appear to serve as exaptation (preadaptation) features for farming. As an easily recognized example, fleshy fruits are, an exaptation to agriculture, as they evolved to recruit a non-human disperser. We hypothesize that the traits of rapid annual growth, self-compatibility, heavy investment in reproduction, high plasticity (wide reaction norms), and rapid evolvability were part of an adaptive syndrome for megafaunal seed dispersal. We review the evolutionary importance that megafauna had for crop and weed progenitors and discuss possible ramifications of their extinction on: (1) seed dispersal; (2) population dynamics; and (3) habitat loss. Humans replaced some of the ecological services that had been lost as a result of late Quaternary extinctions and drove rapid evolutionary change resulting in domestication.

Reimagining the relationship between Gondwanan forests and Aboriginal land management in Australia's "Wet Tropics"

The "Wet Tropics" of Australia host a unique variety of plant lineages that trace their origins to the super-continent of Gondwanaland. While these "ancient" evolutionary records are rightly emphasized in current management of the region, multidisciplinary research and lobbying by Rainforest Aboriginal Peoples have also demonstrated the significance of the cultural heritage of the "Wet Tropics." Here, we evaluate the existing archeological, paleoenvironmental, and historical evidence to demonstrate the diverse ways in which these forests are globally significant, not only for their ecological heritage but also for their preservation of traces of millennia of anthropogenic activities, including active burning and food tree manipulation. We argue that detailed paleoecological, ethnobotanical, and archeological studies, working within the framework of growing national and world heritage initiatives and active application of traditional knowledge, offer the best opportunities for sustainable management of these unique environments in the face of increasingly catastrophic climate change and bushfires.

Individuality, self and sociality of vascular plants

Vascular plants are integrated into coherent bodies via plant-specific synaptic adhesion domains, action potentials (APs) and other means of long-distance signalling running throughout the plant bodies. Plant-specific synapses and APs are proposed to allow plants to generate their self identities having unique ways of sensing and acting as agents with their own goals guiding their future activities. Plants move their organs with a purpose and with obvious awareness of their surroundings and require APs to perform and control these movements. Self-identities allow vascular plants to act as individuals enjoying sociality via their self/non-self-recognition and kin recognition. Flowering plants emerge as cognitive and intelligent organisms when the major strategy is to attract and control their animal pollinators as well as seed dispersers by providing them with food enriched with nutritive and manipulative/addictive compounds. Their goal in interactions with animals is manipulation for reproduction, dispersal and defence. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions

Protein-rich legumes accompanied carbohydrate-rich cereals since the beginning of agriculture and yet their domestication history is not as well understood. Lentil (Lens culinaris Medik. subsp. culinaris) was first cultivated in Southwest Asia (SWA) 8000-10,000 years ago but archeological evidence is unclear as to how many times it may have been independently domesticated, in which SWA region(s) this may have happened, and whether wild species within the Lens genus have contributed to the cultivated gene pool. In this study, we combined genotyping-by-sequencing (GBS) of 190 accessions from wild (67) and domesticated (123) lentils from the Old World with archeological information to explore the evolutionary history, domestication, and diffusion of lentils to different environments. GBS led to the discovery of 87,647 single-nucleotide polymorphisms (SNPs), which allowed us to infer the phylogeny of genus Lens. We confirmed previous studies proposing four groups within it. The only gene flow detected was between cultivated varieties and their progenitor (L. culinaris subsp. orientalis) albeit at very low levels. Nevertheless, a few putative hybrids or naturalized cultivars were identified. Within cultivated lentil, we found three geographic groups. Phylogenetics, population structure, and archeological data coincide in a scenario of protracted domestication of lentils, with two domesticated gene pools emerging in SWA. Admixed varieties are found throughout their range, suggesting a relaxed selection process. A small number of alleles involved in domestication and adaptation to climatic variables were identified. Both novel mutation and selection on standing variation are presumed to have played a role in adaptation of lentils to different environments. The results presented have implications for understanding the process of plant domestication (past), the distribution of genetic diversity in germplasm collections (present), and targeting genes in breeding programs (future).

Anthropogenic Seed Dispersal: Rethinking the Origins of Plant Domestication

It is well documented that ancient sickle harvesting led to tough rachises, but the other seed dispersal properties in crop progenitors are rarely discussed. The first steps toward domestication are evolutionary responses for the recruitment of humans as dispersers. Seed dispersal-based mutualism evolved from heavy human herbivory or seed predation. Plants that evolved traits to support human-mediated seed dispersal express greater fitness in increasingly anthropogenic ecosystems. The loss of dormancy, reduction in seed coat thickness, increased seed size, pericarp density, and sugar concentration all led to more-focused seed dispersal through seed saving and sowing. Some of the earliest plants to evolve domestication traits had weak seed dispersal processes in the wild, often due to the extinction of animal dispersers or short-distance mechanical dispersal.