In the origin of modern humans, hunting of wild animals and gathering of wild plants in nature were the primary subsistence strategies. Yet, about 12,000 years ago, the domestication of plants and animals began. The two main goals of the present chapter are to briefly describe (i) how wild animals were domesticated and (ii) what are the main biological consequences for the major farmed species (cattle, pig, sheep, goat, and horse). During about 98% of their domestication history, domestic animals have been managed in a sustainable way by farmers, followed by a period of strong selection about 200 years ago to produce hundreds of well-defined breeds. A few decades ago, the selection pressures have further increased, leading to a few industrial breeds, which were introduced in numerous countries, most often at the expense of local breeds. Within a few decades, we thus might lose most of the highly valuable farm animal genetic resources that humans have gradually selected over the past millennia. Consequently, priorities should be given to preserve the genetic resources in marginal or rare breeds, and selection programs should aim at restoring the genetic diversity in industrial breeds.
- domesticated animals
- industrial breed
- local breed
Since the origin of modern humans,
The domestication of plants and animals was part of a major transformation in the way of life of an increasing number of human societies, with deep social and spiritual changes, called the Neolithic transition [5, 6]. This also enabled a strong increase of the human population from about 1 million during the millennia before the advent of agriculture  to more than 7 billion today . The increase of human population is spectacular during the past decades (Figure 1), with an additional 4 billion people since 1960 .
In 2010, the world agricultural production reaches more than 7.6 billion tons , representing a three-fold increase compared to 1961 (Figure 2). Globally, less than two-thirds of crop production (on a mass basis) are allocated to human food, versus 35% to animal feed, and 3% for bioenergy or other industrial products . It is, however, important to highlight that global food production relied
The other main consequences of domestication are that the bulk of global agriculture is today based on the culture or farming of a few alien domesticated species that had been progressively introduced in all continents. This has contributed to widespread faunal and floral homogenization . Nevertheless, because alien species are present for a very long period, they are generally not perceived as exogenous or introduced , but rather as part of the natural landscape [16, 17, 18]. This phenomenon has been described as the shifting baseline syndrome . Agriculture is today responsible for the destruction or modification of nearly 40% of the land surface . For instance, about 7 to 11 million km2 of forest have been lost in the past 300 years due to land-use activities, primarily for agricultural expansion and timber extraction . Besides, intensification of agriculture has also resulted in the degradation of water quality in numerous freshwater and coastal ecosystems due to the global use of fertilizers, pesticides, and antibiotics [9, 20]. Modern agriculture is thus generally considered to be the primary destructive force of biodiversity , which has led to the sixth mass extinction . Some scientists even consider that truly wild nature (pristine zones from human impacts) does no longer exist on Earth . In 2002, Crutzen  proposed to assign the term “Anthropocene” to the present geological epoch, supplementing the Holocene, once humans have become an important geochemical force and perhaps the dominant ecological force on the planet. The Anthropocene era could be said to have started in the late eighteenth century . In conclusion, domestication corresponds to a pivotal change in the history not only of humanity but also of the biosphere [5, 6].
The two main goals of the present chapter are to briefly describe (i) how wild animals were domesticated and (ii) what are the main biological consequences for the major farmed species.
2. How were animals domesticated?
Domestication is a long and endless process by which animals become adapted to both humans and captive conditions ([24, 25, 26]; for an overview of definitions of domestication, see ). Three main pathways of domestication have been proposed for land animals: a commensal pathway, a prey pathway, and a directed pathway [6, 28, 29, 30]. In the commensal pathway, the animals themselves played the largest role . The animals first move into an anthropogenic habitat, most likely spurred by an attraction to human waste, and later develop a two-way partnership with humans . Several domesticated species have followed this path, among which are dog (
Species that followed either commensal or prey pathways tend to possess more traits that make them appropriate candidates for domestication. Conversely, species on directed pathways likely possess barriers to domestication that require more knowledge on the part of humans to overcome [28, 31].
Whatever the pathway followed, captive animals began to be domesticated at some point. Yet, as for domestication, there is no consensus today about what a domesticated species is (see  for a review of the main definitions). Nevertheless, most authors considered that a domesticated species is a group of animals reproduced in captivity and modified from their wild congeners . Yet, wild and domesticated animals should not be considered as complementaries (such as true/false, dead/alive) but rather as antonyms (such as long/short, fast/slow) because they represent the extremes of a process and not a simple dichotomy . In other words, there is not a clear biological separation between wild and domesticated animals . In addition, a domesticated animal is neither in a final nor a static status, and thus farmed species are still evolving today, particularly in response to changes in technology and husbandry practices, which themselves are evolving and constantly improving . Conversely, domesticated species can sometimes return to nature, a process known as feralization .
3. How have animals evolved during domestication?
During domestication, five main genetic processes were involved [15, 28, 34], including inbreeding and genetic drift (two uncontrolled processes), natural selection in captivity and relaxation of natural selection (two partially controlled processes), and active selection (one controlled process) [34, 35]. The two uncontrolled processes are due to the limited size of the population (known as inbreeding) and the random changes in gene frequencies (genetic drift). The two partially controlled processes are natural selection in captivity that accounts for selection imposed on captive populations that cannot be attributed to active (or artificial) selection and relaxation of natural selection expectably accompanying the transition from wild to captive environments . At last, the fifth genetic process is controlled, known as active selection, because changes are directional [34, 35].
Domesticated animals have been profoundly modified during domestication. Indeed, the variation range of certain traits within a domesticated species occasionally exceeds that in whole families or even orders [36, 37]. Modifications resulting from domestication concern morphoanatomy, physiology, behavior, and genetics [31, 35, 38, 39, 40]. Behavior is probably the first to have been modified during domestication . Nevertheless, behavioral traits neither appeared nor disappeared during domestication but rather are the response thresholds that changed [34, 35]. One of the most remarkable behavioral changes shared by all domesticates is their tolerance of proximity to (or complete lack of fear of) people [31, 37, 39]. Besides, because humans provide shelter, food, and protection against predators, domesticated animals most often express a lower incidence of antipredator behaviors and show lower motivation for foraging . More generally, mood, emotion, agnostic and affiliative behavior, as well as social communication all have been modified in some way by domestication . Most domesticated animals are also more precocious than their wild counterparts . The activity of their reproductive system became enhanced and relatively uncoupled from the environmental photoperiod, and they all acquired the capacity to reproduce in any season and more often than once a year . At last, the most spectacular and obvious changes concern morphology, among which are the animal size (dwarfs and giants), proportions (fewer vertebrae, shorter tails), color, length and texture of coat, wavy or curly hair, rolled tails, and floppy ears or other manifestations of neoteny (the retention of juvenile features into sexual maturity) [37, 39]. In most domesticated species, head or brain size has decreased . The most illustrative example of such considerable changes is the morphological variations in dogs . These morphological changes (“domestication syndrome”) may all be linked to strong selection for lowered reactivity to external stimuli . At the beginning of the twentieth century, modern breeding programs were initiated, leading to dramatic changes in productivity, e.g., increase laying rate for laying hens or improved feed conservation ratio, meat yield, and growth rate in broiler chickens .
4. A brief history of the major domesticated animals
Even though the decision to consider farmed or captive animals as domesticated is subjective and arbitrary [35, 41], most authors agree that about 40 species around the world that directly or indirectly contribute to agriculture are domesticated; this number varies between 20 and 50 following the definitions used for a domesticated animal [36, 42, 43, 44]. Several of those domesticated species have a distinct scientific name than their wild ancestors .
The 14 most important domesticated mammal species are indicated in Table 1, among which the domestication of the “big five” (cattle, pig, sheep, goat, and horse) [3, 4] are further described below. For the five most valuable species, the domestication resulted in the creation of hundreds of breeds, particularly in the past centuries [42, 45, 46]. In France, the article D.653.9 of the rural code defines breed for ruminant species as “a group of animals that share sufficient common features to be considered homogeneous by one or several groups of breeders that agree on the broodstock renewal and induced changes, including the international level“ . Breeds have therefore both a biological sense (common features) and a social acceptance (group of breeders); the relative importance of the latter increased in the past years, for scientists as well as in the application of policies .
The wild ancestor of cattle is a group of races of the now extinct aurochs
|Common name||Scientific names||Partial list of potential wild progenitors (in bold the main one)||Approximate date of domestication: BP||Number of breeds||Pathway to domestication|
|Bactrian camel||4500||6||Directed pathway|
|Llama and alpaca||6000||2 + 2||Prey pathway|
|Donkey or ass||6000||70||Directed pathway|
|Water buffalo||6000||70||Prey pathway|
|Bali cattle||Prey pathway (?)|
|Mithan||Prey pathway (?)|
|Authors or editors||Date||Title||Ref.|
|Darwin CR||1859||On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life|||
|Darwin CR||1868||The Variation of Animals and Plants under Domestication|||
|Clutton-Brock J||1987||The Natural History of Domesticated Mammals|||
|Digard JP||1990||L’homme et les animaux domestiques: Anthropologie d’une passion|||
|Diamond J||1997||Guns, Germs, and Steel: The Fates of Human Societies|||
|Guillaume J||2010||Ils ont domestiqué plantes et animaux: Prélude à la civilisation|||
|Clutton-Brock J||2012||Animals as Domesticates: A World View Through History|||
|Gepts et al.||2012||Biodiversity in Agriculture: Domestication, Evolution, and Sustainability|||
|Vigne JD||2012||Les débuts de l’élevage|||
|Wuerthner et al.||2014||Keeping the Wild: Against the Domestication of Earth|||
|Francis RC||2015||Domesticated: Evolution in a Man-Made World|||
|Alves and Albuquerque||2018||Ethnozoology: Animals In Our Lives|||
|Scanes and Toukhsati||2018||Animals and Human Society|||
The wild ancestor of domestic pigs is boar
The wild ancestors of the domestic sheep are probably the mouflon (
The wild ancestor of goat is the bezoar,
The wild ancestor of domestic horse is the now extinct,
5. Final considerations
Ever since Darwin, the study of domestication has puzzled scientists . Hundreds of articles are published each year [33, 39], as well as books, among which some are listed in Table 2. Despite this interest, both the words “domestication” and “domestic animal” remain confusing and poorly defined . For domestication, this is mainly due to the inherent difficulty in assigning static terms to a process involving long-term and continuous change . For “domestic animal,” this is because this sort of dichotomous perspective wild/domestic is false and obscures the existence of transitional forms [32, 36, 73, 74, 75]. This is why the concept of “domestication level” was proposed for fish to describe more accurately the diversity of production methods as a continuum , from fishing up to the rearing of genetically improved animals [24, 25, 41, 76, 77]. This concept could be applied to other animals [26, 27] and may help describing the evolution of farmed species through both space and time in the future [36, 73].
Traditionally, the process of domestication was assumed to be initiated by humans, involving strong bottlenecks in the domestic population (corresponding to founder events due to the selection of only a few individuals at the beginning of the process) and reproductive isolation between wild and domestic forms [52, 67]. However, a growing body of archaeological, genetic, and ethnohistorical evidence suggests that long-term gene flow between wild and domestic stocks was much more common than previously expected, and selective breeding of females was largely absent during the early phases of animal domestication [52, 67]. Therefore, complete separation between wild and domestic populations was relatively late and region-specific . These findings challenge assumptions about severe genetic bottlenecks during domestication and interpretations of genetic variability in terms of multiple instances of domestication and raise new questions regarding ways in which behavioral and phenotypic domestication traits were developed and maintained [52, 72]. The identity of the wild progenitor (or progenitors) of most domestic mammals remains also unclear because (i) the potential wild progenitors are often able to interbreed and produce fertile offspring with the domesticated congeners and (ii) many domestic animals can produce viable offspring with a host of wild, closely related sister taxa . Therefore, the intuitive notion that each modern domestic animal (when discussed as a global population) is descended solely from a single wild species is almost certainly incorrect, and the genetic ancestry of domestics is likely to be relatively complex [32, 40].
Domesticated species are the result of a long and endless process that started millennia ago (Table 1). During about 98% of their domestication history, farm animals have been managed in a sustainable way by farmers, which lead to animals well adapted to local conditions [49, 50]. Yet, the situation changed dramatically 200 years ago as animals began to be selected for the same phenotypic characteristics to produce hundreds of well-defined breeds (Table 1), and reproduction among breeds was seriously reduced, leading to the fragmentation of the initial gene pool [49, 50, 70]. A few decades ago, the selection pressures were increased further, particularly with the use of artificial insemination, leading to a few industrial breeds with very high performances [49, 50, 70]. In the United States, the average milk production/cow of dairy cows increased by 1287 kg between 1993 and 2002, and 708 kg of this increase, or 55%, was due to genetics . Interestingly, until the mid-1980s, most of the increase in milk yield was the result of improved management, in particular better application of nutritional standards and improved quality of rough age . Since then, genetics became the major factor as a result of effective use of artificial insemination, intense selection based on progeny testing of bulls, and worldwide distribution of semen from bulls with high genetic merit for production . This results in that, despite their total number of individuals, numerous industrial breeds have low effective population sizes [49, 50, 70]. This might explain that apart from a highly favorable increase in production, present-day selection for high production efficiency in livestock species in many cases was accompanied by undesirable side effects for several physiological, immunological, and reproduction traits [78, 79]. A new breeding goal aimed at improving fitness and tolerance of metabolic stress is necessary to prevent the decrease in the quality of life of farmed species and instead, perhaps, enhance it [70, 78, 79, 80]. More generally, an alternative to breeding for specific traits is to target “robustness” and “resilience,” with the former focusing on current variation among environments and the latter on future variation . Management strategies should be used to address short-term challenges from changing environments, and genetic selection should be used to address long-term problems . Another solution might be to crossbreed domesticated animals either with their wild ancestor (if they still exist) or with wild relatives; it is therefore also urgent to properly assess the potential of the wild relatives as genetic resources for agriculture, and because most are endangered, actions should be implemented to preserve them . Local breeds (present in only one country) in marginal areas are also seriously endangered [49, 50, 80]. For instance, in Europe more than 40% of livestock breeds are currently estimated to be endangered . Farmers are often forced to abandon their traditional breeds and to raise more competitive industrial breeds [40, 83]. As a consequence, many locally adapted breeds have already disappeared [49, 50, 82]. Such a phenomenon can be very fast, and a valuable traditional breed can be lost within a decade . Furthermore, even in less-developed countries, the introgression of genes from industrial breeds seriously compromises the long-term persistence of genetic resources in locally well-adapted breeds [49, 50, 83]. Adaptive traits may be rapidly lost by poorly designed crossbreeding, leading to dilution of important adaptive loci of traditional breeds. Traits such as resistance to local infectious and parasitic diseases, adaptation to poor forage, homing, and gregarious behavior can be rapidly lost and difficult to rescue . According to the FAO, about 300 of 6000 breeds of farm animals have become extinct over the past 15 years, and 1350 currently face extinction in the near future [42, 50].
In conclusion, within a few decades, we might lose most of the highly valuable farm animal genetic resources that humans have gradually selected over the past millennia [45, 49, 50, 72]. Subsidies should therefore be urgently given to help farmers who contribute to the
Conflict of interest
The author declares no conflict of interest.