How traits evolve differently in natural vs domestic conditions 

Whether it happened artificially (as is in the farm-fox experiments that selected for tameability) or naturally (as a theory for how dogs evolved) or a combination thereof, domestication is an evolutionary process that involves a changing environment (new situations) influencing allele frequency favoring certain mutations that allow the animal to breed more in the new niche. But while the end result may be the same (even indistinguishable) the two processes proceed differently.       (Trut et al 2004; Fox 1978). 

Natural conditions

Under natural conditions, a new trait (such as dogs’ ability to read human social cues) that has occurred through mutation allows an animal to fill a new niche or take advantage of a new situation.

The case of humans and dogs

The appearance of groups of humans allowed dogs to follow these groupings and get access to food and possible predator protection. If a few dogs who had this new ability were more successful (in terms of number of offspring) then this could lead to extinction of the first species in favor of the new one or speciation. If a new species broke off from the main group, change in niche environments between the two species might reduce or eliminate the possibility of interbreeding. The new species would then be concentrated in the new environment leading to further selective pressure to adapt that niche. This would lead to the honing of traits that encouraged survival and reproduction for those animals. (Dogs became more and more in tune with humans in order to better their use of human cues to find food.)  Depending on the future environmental conditions this could lead one species to survive and dominate the other or the two to coexist in separate environments. (Hare & Tomasello 2005).

Domestic conditions

 Under domestic conditions, a change in human culture provides a new niche for animals with certain mutations that are better adapted to the new environment.  These animals may be bred by humans for food, work, protection, and transportation.  The same selection pressures are exerted on species with some animals having better access to food (fed by humans), lower probability of death (protection and veterinary care), and more ability to reproduce (directed animal husbandry). This can cause speciation or whole scale change of a species if noncompetitive members cannot survive in other environments or if their previous niches no longer exist (due to human action like deforestation).  (Diamond 2002).

Directed selection

Humans may also exert differing pressures on different members of one species (dog breeds) leading to different niches and functions for different members. Another possibility is that humans will select on the basis of one trait or closely connected group of traits in order to further a specific outcome that can unexpectedly influence other aspects of the animals’ life and adaptation (morphological changes in the foxes). This can cause the species to be divided into breeds based on physical rather than genetic traits and exert reproductive control.  Matings may then be confined by both artificial barriers (humans, i.e. kennel clubs) or by the animal themselves and differences in physical characteristics.   (Saetre et al 2006).