Domestication
Domestication is a multi-generational mutualistic relationship between humans and other organisms, in which humans take over control and care to obtain a steady supply of resources including food. The process was gradual and geographically diffuse, based on trial and error. The first animal to be domesticated was the dog, as a commensal, at least 15,000 years ago. Other animals including goat, sheep, and cow were domesticated starting around 11,000 years ago. Among birds, the chicken was domesticated in East Asia, seemingly for cockfighting, some 7,000 years ago. The horse came under domestication around 5,500 years ago in central Asia as a working animal. Among invertebrates, the silkworm and the western honey bee were domesticated over 5,000 years ago for silk and honey respectively. The domestication of plants began around 13,000–11,000 years ago with cereals such as wheat and barley in the Middle East, alongside crops such as lentil, pea, chickpea, and flax. Rice was first cultivated in China some 13,500 to 8,200 years ago. Beginning around 10,000 years ago, Indigenous peoples in the Americas began to cultivate peanuts, squash, cotton, and cassava. In Africa, crops such as sorghum were domesticated. Agriculture developed in some 13 centres around the world, domesticating different crops and animals. Domestication affected genes for behaviour in animals, making them less aggressive. In plants, domestication affected genes for morphology, such as increasing seed size and stopping the shattering of seed-heads such as in wheat. Such changes both make domesticated organisms easier to handle, and reduce their ability to survive in the wild. Definitions 

Domestication (not to be confused with the taming of an individual animal), is from the Latin , 'belonging to the house'. The term remained loosely defined until the 21st century, when the American archaeologist Melinda A. Zeder defined it as a long-term relationship in which humans take over control and care of another organism to gain a predictable supply of a resource, resulting in mutual benefits. She noted further that it is not synonymous with agriculture, since agriculture depends on domesticated organisms, but does not automatically result from domestication. Domestication syndrome is the suite of phenotypic traits which arose during the initial domestication process, and which distinguish crops from their wild ancestors. It can also mean a set of differences now observed in domesticated animals, not necessarily reflecting the initial domestication process. The differences include increased docility and tameness, coat color changes, reductions in tooth size, changes in craniofacial morphology, alterations in ear and tail form (e.g., floppy ears), changes in estrus cycles, changed levels of adrenocorticotropic hormone and neurotransmitters, prolongations in juvenile behavior, and reductions in brain size and of particular brain regions. Cause and timing 

The domestication of animals and plants was triggered by the climatic and environmental changes that occurred after the peak of the Last Glacial Maximum  and which continue to this present day. These changes made obtaining food by hunter-gathering difficult. The first domesticate was the dog at least 15,000 years ago. The Younger Dryas 12,900 years ago was a period of intense cold and aridity that put pressure on humans to intensify their foraging strategies. By the beginning of the Holocene from 11,700 years ago, favorable climatic conditions and increasing human populations led to small-scale animal and plant domestication, which allowed humans to augment their food supply. The appearance of the domestic dog in the archaeological record was followed by domestication of livestock and of crops such as wheat and barley, the invention of agriculture, and the transition of humans from foraging to farming in different places and times across the planet. In the Fertile Crescent 10,000–11,000 years ago, zooarchaeology indicates that goats, pigs, sheep, and taurine cattle were the first livestock to be domesticated. Two thousand years later, humped zebu cattle were domesticated in what is today Baluchistan in Pakistan. In East Asia 8,000 years ago, pigs were domesticated from wild boar that were genetically different from those found in the Fertile Crescent. The horse was domesticated on the Central Asian steppe 5,500 years ago. The cat was domesticated in Egypt 4,000 years ago. With a steady supply of food from farming, relying on domesticated plant and animal species, major changes, described as the Neolithic transition, created agricultural societies across Eurasia, North Africa, and South and Central America. This involved major changes to human society: higher-density populations in the centers of domestication, the expansion of agricultural economies, and the development of urban communities. Animals

Desirable traits 

The domestication of animals is the relationship between animals and humans who have influence on their care and reproduction. In his 1868 book The Variation of Animals and Plants Under Domestication, Charles Darwin recognized the small number of traits that made domestic species different from their wild ancestors. He was also the first to recognize the difference between conscious selective breeding in which humans directly select for desirable traits, and unconscious selection in which traits evolve as a by-product of natural selection or from selection on other traits. There is a difference between domestic and wild populations; some of these differences constitute the domestication syndrome, traits presumed essential in the early stages of domestication, while others represent later improvement traits. Domesticated animals tend to be smaller and less aggressive than their wild counterparts; other common traits are floppy ears, a smaller brain, and a shorter muzzle. Domestication traits are generally fixed within all domesticates, and were selected during the initial episode of domestication of that animal or plant, whereas improvement traits are present only in a proportion of domesticates, though they may be fixed in individual breeds or regional populations. Certain animal species, and certain individuals within those species, make better candidates for domestication because of their behavioral characteristics:

 The size and organization of their social structure
 The availability and the degree of selectivity in their choice of mates
 The ease and speed with which the parents bond with their young, and the maturity and mobility of the young at birth
 The degree of flexibility in diet and habitat tolerance
 Responses to humans and new environments, including reduced flight response and reactivity to external stimuli. Mammals 

The beginnings of animal domestication involved a protracted coevolutionary process with multiple stages along different pathways. There are three proposed major pathways that most animal domesticates followed into domestication: 

 commensals, adapted to a human niche (e.g., dogs, cats, possibly pigs)
 prey animals sought for food (e.g., sheep, goats, cattle, water buffalo, yak, pig, reindeer, llama and alpaca)
 animals targeted for draft and riding (e.g., horse, donkey, camel). Humans did not intend to domesticate animals from either the commensal or prey pathways, or at least they did not envision a domesticated animal would result from it. In both of those cases, humans became entangled with these species as the relationship between them intensified, and humans' role in their survival and reproduction led gradually to formalised animal husbandry. Although the directed pathway for draft and riding animals proceeded from capture to taming, the other two pathways are not as goal-oriented, and archaeological records suggest that they took place over much longer time frames. Unlike other domestic species selected primarily for production-related traits, dogs were initially selected for their behaviors. The dog was domesticated long before other animals, becoming established across Eurasia before the end of the Late Pleistocene era, well before agriculture. The archaeological and genetic data suggest that long-term bidirectional gene flow between wild and domestic stocks – such as in donkeys, horses, New and Old World camelids, goats, sheep, and pigs – was common. Human selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars into pigs, and created domestication islands in the genome. The same process may apply to other domesticated animals. Birds 

Domesticated birds principally mean poultry, raised for meat and eggs: some Galliformes (chicken, turkey, guineafowl) and Anseriformes (waterfowl: ducks, geese, and swans). Also widely domesticated are cagebirds such as songbirds and parrots; these are kept both for pleasure and for use in research. The domestic pigeon has been used both for food and as a means of communication between far-flung places through the exploitation of the pigeon's homing instinct; research suggests it was domesticated as early as 10,000 years ago. Chicken fossils in China have been dated to 7,400 years ago. The chicken's wild ancestor is Gallus gallus, the red junglefowl of Southeast Asia. The species appears to have been kept initially for cockfighting rather than for food. Invertebrates 

Two insects, the silkworm and the western honey bee, have been domesticated for over 5,000 years, often for commercial use. The silkworm is raised for the silk threads wound around its pupal cocoon; the western honey bee, for honey, and, lately, for pollination of crops. Several other invertebrates have been domesticated, both terrestrial and aquatic, including some such as Drosophila melanogaster fruit flies and the freshwater cnidarian Hydra for research into genetics and physiology. Few have a long history of domestication. Most are used for food or other products such as shellac and cochineal. The phyla involved are Cnidaria, Platyhelminthes (for biological control), Annelida, Mollusca, Arthropoda (marine crustaceans as well as insects and spiders), and Echinodermata. While many marine molluscs are used for food, only a few have been domesticated, including squid, cuttlefish and octopus, all used in research on behaviour and neurology. Terrestrial snails in the genera Helix are raised for food. Several parasitic or parasitoidal insects including the fly Eucelatoria, the beetle Chrysolina, and the wasp Aphytis are raised for biological control. Conscious or unconscious artificial selection has many effects on species under domestication; variability can readily be lost by inbreeding, selection against undesired traits, or genetic drift, while in Drosophila, variability in eclosion time (when adults emerge) has increased. Plants 

Humans foraged for wild cereals, seeds and nuts thousands of years before they were domesticated; wild wheat and barley, for example, were gathered in the Levant at least 23,000 years ago. Neolithic societies in West Asia first began to cultivate and then domesticate some of these plants around 13,000 to 11,000 years ago. The founder crops of the West Asian Neolithic included cereals (emmer, einkorn wheat, barley), pulses (lentil, pea, chickpea, bitter vetch), and flax. Other plants were independently domesticated in other centers of origin in some 24 different regions of the Americas, Africa, and Asia (the Middle East, South Asia, the Far East, and New Guinea and Wallacea); in some thirteen of these regions people began to cultivate grasses and grains. Rice was first cultivated in East Asia. Sorghum was widely cultivated in sub-Saharan Africa, while peanuts, squash, cotton, and cassava were domesticated in the Americas. Continued domestication was gradual and geographically diffuse – happening in many small steps and spread over a wide area – on the evidence of both archaeology and genetics. It was a process of intermittent trial and error, and often resulted in diverging traits and characteristics. Whereas domestication of animals impacted most on the genes that controlled behavior, that of plants impacted most on the genes that controlled morphology (seed size, plant architecture, dispersal mechanisms) and physiology (timing of germination or ripening), as in the domestication of wheat. Wild wheat shatters and falls to the ground to reseed itself when ripe, but domesticated wheat stays on the stem for easier harvesting. This change was possible because of a random mutation in the wild populations at the beginning of wheat's cultivation. Wheat with this mutation was harvested more frequently and became the seed for the next crop. Therefore, without realizing, early farmers selected for this mutation. The result is domesticated wheat, which relies on farmers for its reproduction and dissemination. Differences from wild plants 

Domesticated plants differ from their wild relatives in many ways, including

 lack of shattering such as of cereal ears (ripe heads), loss of fruit abscission
 less efficient breeding system (e.g. without normal pollinating organs, making human intervention a requirement), larger seeds with lower success in the wild, or even sterility (e.g. seedless fruits) and therefore only vegetative reproduction
 better palatability (e.g. higher sugar content, reduced bitterness), better smell, and lower toxicity
 edible part larger, e.g. cereal grains or fruits 
 edible part more easily separated from non-edible part
 increased number of fruits or grains
 altered colour, taste, and texture
 daylength independence
 determinate growth
 reduced or no vernalization
 less seed dormancy. In addition, it has been suggested that plant defences against herbivory, such as thorns, spines, and prickles, poison, protective coverings and sturdiness, have been reduced in domesticated plants. This would make them more likely to be eaten by herbivores unless protected by humans, but there is only weak support for most of this. Farmers did select for reduced bitterness and lower toxicity, and for food quality, which likely increased crop palatability to herbivores as to humans. However survey of 29 plant domestications found that crops were as well-defended against two major insect pests (beet armyworm and green peach aphid) both chemically (e.g. with bitter substances) and morphologically (e.g. with toughness) as their wild ancestors. Changes to plant genome 

During domestication, crop species undergo intense artificial selection that alters their genomes, establishing core traits that define them as domesticated, such as increased grain size. Comparison of the coding DNA of chromosome 8 in rice between fragrant and non-fragrant varieties showed that aromatic and fragrant rices, including basmati and jasmine, are derived from an ancestral rice domesticate that suffered a deletion in exon 7 which altered the coding for betaine aldehyde dehydrogenase (BADH2). Comparison of the potato genome with that of other plants located genes for resistance to potato blight caused by Phytophthora infestans. In coconut, genomic analysis of 10 microsatellite loci (of noncoding DNA) found two episodes of domestication based on differences between individuals in the Indian Ocean and those in the Pacific Ocean. The coconut experienced a founder effect, where a small number of individuals with low diversity founded the modern population, permanently losing much of the genetic variation of the wild population. Population bottlenecks which reduced variation throughout the genome at some later date after domestication are evident in crops such as pearl millet, cotton, common bean and lima bean. In wheat, domestication involved repeated hybridization and polyploidy. These steps are large and essentially instantaneous changes to the genome and the epigenome, enabling a rapid evolutionary response to artificial selection. Polyploidy increases the number of chromosomes, bringing new combinations of genes and alleles, which in turn enable further changes such as by chromosomal crossover. Impact on plant microbiome 

The microbiome, the collection of microorganisms inhabiting the surface and internal tissue of plants, is affected by domestication. This includes changes in microbial species composition and diversity. Plant lineage, including speciation, domestication, and breeding, have shaped plant endophytes (phylosymbiosis) in similar patterns as plant genes. Fungi 

Several species of fungi have been domesticated for use directly as food, or in fermentation to produce foods and drugs. The cultivated mushroom Agaricus bisporus is widely grown for food. The yeast Saccharomyces cerevisiae have been used for thousands of years to ferment beer and wine, and to leaven bread. Mould fungi including Penicillium are used to mature cheeses and other dairy products, as well as to make drugs such as antibiotics. Effects

On domestic animals 

Selection of animals for visible traits may have undesired consequences for the genetics of domestic animals. A side effect of domestication has been zoonotic diseases. For example, cattle have given humanity various viral poxes, measles, and tuberculosis; pigs and ducks have contributed influenza; and horses have brought the rhinoviruses. Many parasites, too, have their origins in domestic animals. Alongside these, the advent of domestication resulted in denser human populations which provided ripe conditions for pathogens to reproduce, mutate, spread, and eventually find a new host in humans. On society 

Jared Diamond in his book Guns, Germs, and Steel describes the universal tendency for populations that have acquired agriculture and domestic animals to develop a large population and to expand into new territories. He recounts migrations of people armed with domestic crops overtaking, displacing or killing indigenous hunter-gatherers, whose lifestyle is coming to an end. Anarcho-primitivism critiques domestication as destroying the supposed primitive state of harmony with nature in hunter-gatherer societies, and replacing it, possibly violently or by enslavement, with a social hierarchy as property and power emerged. The dialectal naturalist Murray Bookchin has argued that domestication of animals in turn meant the domestication of humanity, both parties being unavoidably altered by their relationship with each other. The sociologist David Nibert asserts that the domestication of animals involved violence against animals and damage to the environment. This in turn, he argues, corrupted human ethics, and paved the way for "conquest, extermination, displacement, repression, coerced and enslaved servitude, gender subordination and sexual exploitation, and hunger." On diversity 

In 2016, a study found that humans have had a major impact on global genetic diversity as well as extinction rates, including a contribution to megafaunal extinctions. Pristine landscapes no longer exist and have not existed for millennia, and humans have concentrated the planet's biomass into useful plants and animals. Domesticated ecosystems provide food, reduce predator and natural dangers, and promote commerce, but have also resulted in habitat loss and extinctions commencing in the Late Pleistocene. Ecologists and other researchers are advised to make better use of the archaeological and paleoecological data available for gaining an understanding the history of human impacts before proposing solutions. 