Introduction

Michèle TIXIER-BOICHARD1 and Georges PELLETIER2,3

1GABI, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France

2Académie des sciences, Paris, France

3Académie d’agriculture de France, Paris, France

Based on a definition

Domestic, in the first sense, means belonging to the house, in Latin “domus”. Thus, for a living being, it means living in a home, in the broadest sense, of man, being raised and fed there. The domestication of animals, plants and microorganisms is therefore a process of adapting individuals, then their descendants, to an environment that is modified by human groups. This adaptation is associated with hereditary transformations that are conducive to their exploitation, which are expressed, for example, in an animal’s docile nature or the limitation of the spontaneous dispersal of cereal grains. In some cases, the species disappears in the wild and is only represented by domesticated types. Domestication can thus be seen as evolutionary pressure. A generic definition of domestication has been proposed by the Convention on Biological Diversity1 as follows: “‘Domesticated or cultivated species’ means species in which the evolutionary process has been influenced by humans to meet their needs”.

The transition from the wild to the domesticated state is just a starting point, because as human needs continue to evolve, so does the adaptation and management of domesticated species. Domestication can thus be seen as a process of accumulating heritable modifications to the characteristics of a group of individuals, enabling them to better meet the needs of our species, not only for survival, but also for pleasure, or for cultural or symbolic reasons. These genetic transformations of the species we have chosen, and the history of their exploitation for a variety of needs, have led to a diversification of animal breeds and plant varieties, in addition to strains of microorganisms involved in the manufacture of many fermented foods, such as beer, wine, bread, cheese and more. The history of their domestication has become increasingly well documented since the advent of modern DNA analysis technologies, revealing a plethora of strains and species whose ability to evolve and exchange genes contributes to the quality of these products.

Understanding domestication

When and where did domestication begin? How did it happen?

The history of domestication is intimately linked to human history or, more accurately, to the history of different human groups scattered across the planet. Archaeological digs enable us to reconstruct the past of certain species by uncovering their remains and using all the technical resources of archaeobotany and archaeozoology,2 from morphological description to various types of analysis. These include, for example, carbon isotope content for dating, or DNA sequences that can be extracted to reveal their relationship with today’s domesticated species.

In terms of the evolution of modern man, whose emergence can be traced back some 300,000 years to Africa, before migrating to the Eurasian continent and later to Australia and the Americas, the first domestications only appeared very late, in the last two tens of thousands of years before us: dog, man’s oldest companion, is thought to have been domesticated for at least 25,000 years. Over the last 12,000 years, plant species have undergone new types of genetic selection, corresponding to the needs of populations and leading to the emergence of agricultural societies in various parts of the world (Purruganan and Fuller 2009). Up until then, man had already been using plant and animal resources through gathering and hunting. Thus, the use of selectively harvested wild cereals, which spontaneously seeded and invaded areas occupied by populations, shows a first stage of co-evolution between man and a species used to make food. Evidence of this can be found in the Paleolithic period, like the case of millet in northern China 28,000 years ago, or barley and wheat, with potential signs of cultivation 23,000 years ago by hunter-gatherers who set up sedentary sites in the Middle East. The beginnings of bread-making are confirmed to have started 14,600 years ago, well before the domestication of wheat. The satisfaction of these needs led to new economic activity involving work in the fields, and the storage and processing of harvests. The seasonal nature of cereals led to the construction of storage facilities. The granaries that precede the emergence of domestication by at least 1,000 years represent a critical change in the relationship between humans and plant foods, with new social organizations of sedentary communities and the emergence of agriculture (Willcox and Stordeur 2012; Vigne 2015).

Different species have been involved in different regions on all continents, identified as hotbeds of domestication. Examples include the Fertile Crescent in the Middle East (wheat, barley, lentils, peas, chickpeas, ruminants, pigeon, cat and cochineal), China and Southeast Asia (rice, millet, soy, pig, chicken and duck), sub-Saharan Africa (sorghum, rice, millet and faba bean), Mesoamerica (corn, bean, pumpkin and turkey) and the Andes (potato, bean, quinoa and llama). Domestication initiated in one region is generally followed by a migration phase, as human populations travel with their seeds and animals. For example, many plant species were consumed by hunter-gatherers in the Amazon basin. Once domesticated, these species were gradually spread to other regions of the world, following human migrations or, more recently, following the discovery of America, leading to the exploitation in Europe of sunflowers, squash, pumpkins, corn, manioc, taro, potatoes, tomatoes, sweet potatoes, beans, cotton plants and so on.

The motivations behind domestication are certainly diverse. The controlled availability of cereals (and legumes) that could be stored, as well as the possibility of cooking particular foods (wheat bread) or alcoholic beverages (fermented barley) could be, more than a quest for calories, determining factors in the choice of these two main cereals cultivated in the Middle East, whose characteristics are not found in other wild grasses. Participating in the provisioning of social feasts in a region where, at the outset, there was no evidence of demographic pressure, and where fruits and nuts were abundant, a growing cultural interest in these species would have been a determining factor. In the case of animals, three modalities have been proposed to describe domestication (Larson and Fuller 2014). The commensal pathway corresponds to the case of an animal species living in the vicinity of humans with mutual benefit and involves no human intention. The other two pathways involve human intention, with either the predatory pathway, motivated by the need to obtain supplementary food resources (as a possible reaction to over-hunting), or the directed pathway, for any other intention, such as transport or distraction. However, these three pathways are not mutually exclusive: it is likely that domestication first followed a commensal or predatory path before humans acquired the intention of influencing or modifying an animal species for their own benefit.

The processes of domestication and selection have created ever-closer links between agriculture and society, accompanied by changes in human society. Increased yields have made agricultural production systems more dependent on continuous investment in labor, leading to a form of servitude. The domestication of the horse had a major impact on the mobility of human populations, while that of cattle had a major impact on work capacity in the fields.

The genetics of domestication

Which species have been domesticated? How can we identify wild ancestors? What specific morphological or physiological properties characterize it? What genes and gene modifications are involved? Have domesticated organisms been particularly isolated or have they maintained genetic exchanges with their wild ancestor (Hunter 2018)?

Analysis of the phylogeny of animal and plant species does not show a random distribution of domesticated species. This is particularly clear in the case of animals, where it can be seen that domesticated mammals, known as “cash crops”, are derived from only a small fraction of the phylogenetic and phenotypic diversity of mammals, with an over-representation of the order Artiodactyla (Bovidae: cattle, goats, sheep; Suidae: pigs, etc.), and a few species from the orders Rodentia (guinea pig), Lagomorpha (rabbit) and Perissodactyla (horse, donkey). The other domestic species are essentially from the order Carnivora, phylogenetically close to Artiodactyla and Perissodactyla (in the Ferungulata group). Some authors have jointly analyzed the phylogenetic position and biological or ecological particularities of domesticated species, whether they be animal or plant, and have concluded that certain species are predisposed to others (Milla et al. 2018). The domestication of different cereals (wheat, barley, rice, corn, sorghum and millet), characterized by the loss of spontaneous grain dispersal and dormancy, as well as an increase in grain size, has given rise to the concept of a “domestication syndrome”: common characteristics based on a limited number of mutations, but not implying an identity of these mutations. This concept is only...