Phylogeny
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).
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