Domestication syndrome

Domestication syndrome refers to a number of phenotypic traits that appear in many domesticated animals. These also appeared in the domesticated silver fox that is the result of Dmitry Belyayev's breeding experiment. These traits may include floppy ears, variations to coat colour, a smaller brain, and a shorter muzzle.
Origin.
Charles Darwin’s study of The Variation of Animals and Plants Under Domestication in 1868 identified behavioural, morphological, and physiological traits that are shared by domestic animals, but not by their wild ancestors. These shared traits became known as the domestication syndrome. These traits include tameness, docility, floppy ears, altered tails, novel coat colours and patterns, reduced brain size, reduced body mass and smaller teeth. Other traits include changes in craniofacial morphology, alterations to the endocrine system, and changes to the female estrous cycles including the ability to breed all year-round. 
Research indicates that neural crest cells may have been modified by domestication, which then led to those traits that are common across many domesticated animal species.
Challenge.
In 2015, canine researcher Raymond Coppinger found historical evidence that Belyayev's foxes originated in fox farms on Prince Edward Island and had been bred there for fur farming since the 1800s, and that the traits demonstrated by Belyayev had occurred in the foxes prior to the breeding experiment. In 2019, a further study found that the results of the "Farm fox experiment" had been overstated, based on historical records and DNA analysis. This finding questions the existence of domestication syndrome in animals and suggests that other theories need to be considered, including adaptations to a human-modified environment.
Although the soundness of the domestication syndrome, and the extent to which the Belyaev experiment could be used as evidence to support its existence, has been questioned, the hypothesis that neural crest genes underlie some of the phenotypic differences between domestic and wild horses and dogs is supported by the functional enrichment of candidate genes under selection.
Cause.
In 2018, a study identified 429 genes that differed between modern dogs and modern wolves. As the differences in these genes could also be found in ancient dog fossils, these were regarded as being the result of the initial domestication and not from recent breed formation. These genes are linked to neural crest and central nervous system development. These genes affect embryogenesis and can confer tameness, smaller jaws, floppy ears, and diminished craniofacial development, which distinguish domesticated dogs from wolves and are considered to reflect domestication syndrome. The study proposes that domestication syndrome is caused by alterations in the migration or activity of neural crest cells during their development. The study concluded that during early dog domestication, the initial selection was for behavior. This trait is influenced by those genes which act in the neural crest, which led to the phenotypes observed in modern dogs.
In humans.
A dog's cranium is 15% smaller than an equally heavy wolf's, and the dog is less aggressive and more playful. Other species pairs show similar differences. Bonobos, like chimpanzees, are a close genetic cousin to humans, but unlike the chimpanzees, bonobos are not aggressive and do not participate in lethal inter-group aggression or kill within their own group. The most distinctive features of a bonobo are its cranium, which is 15% smaller than a chimpanzee's, and its less aggressive and more playful behavior. In other examples, the guinea pig's cranium is 13% smaller than its wild cousin the cavy, and domestic fowl show a similar reduction to their wild cousins. Possession of a smaller cranium for holding a smaller brain is a telltale sign of domestication. Bonobos appear to have domesticated themselves. In the farm fox experiment, humans selectively bred foxes against aggression, causing domestication syndrome. The foxes were not selectively bred for smaller craniums and teeth, floppy ears, or skills at using human gestures, but these traits were demonstrated in the friendly foxes. Natural selection favors those that are the most successful at reproducing, not the most aggressive. Selection against aggression made possible the ability to cooperate and communicate among foxes, dogs and bonobos. Perhaps it did the same thing for humans. The more docile animals have been found to have less testosterone than their more aggressive counterparts, and testosterone controls aggression and brain size. One researcher has argued that in becoming more social, we humans have developed a smaller brain than those of humans 20,000 years ago.
In 2017, a researcher proposes that humans show the same domestication syndrome traits that can be found in other domesticated animals, which supports the theory of human self-domestication.