Co-speciation

Biotrophic parasitism is a common mode of life that has arisen independently many times in the course of evolution. Depending on the definition used, as many as half of all animals have at least one parasitic phase in their life cycles,^[10] and it is also frequent in plants and fungi. Moreover, almost all free-living animals are host to one or more parasite taxa.^[10]

Restoration of a Tyrannosaurus with parasite infections. A 2009 study showed that holes in the skulls of several specimens might have been caused by Trichomonas-like parasites^[11]

Parasites evolve in response to defense mechanisms of their hosts. Examples of host defenses include the toxins produced by plants to deter parasitic fungi and bacteria, the complex vertebrate immune system, which can target parasites through contact with bodily fluids, and behavioral defenses. An example of the latter is the avoidance by sheep of open pastures during spring, when roundworm eggs accumulated over the previous year hatch en masse. As a result of these and other host defenses, some parasites evolve adaptations that are specific to a particular host taxon and specialize to the point where they infect only a single species. Such narrow host specificity can be costly over evolutionary time, however, if the host species becomes extinct. Thus, many parasites are capable of infecting a variety of host species that are more or less closely related, with varying success.
Host defenses also evolve in response to attacks by parasites. Theoretically, parasites may have an advantage in this evolutionary arms race because of their more rapid generation time. Hosts reproduce less quickly than parasites, and therefore have fewer chances to adapt than their parasites do over a given span of time.
In some cases, a parasite species may coevolve with its host taxa. In theory, long-term coevolution should lead to a relatively stable relationship tending to commensalism or mutualism, in that it is in the evolutionary interest of the parasite that its host thrives. A parasite may evolve to become less harmful for its host or a host may evolve to cope with the unavoidable presence of a parasite to the point that the parasite's absence causes the host harm. For example, although animals infected with parasitic worms are often clearly harmed, and therefore parasitized, such infections may also reduce the prevalence and effects of autoimmune disorders in animal hosts, including humans.^[12]
The presumption of a shared evolutionary history between parasites and hosts can sometimes elucidate how host taxa are related. For instance, there has been dispute about whether flamingos are more closely related to the storks and their allies, or to ducks, geese and their relatives. The fact that flamingos share parasites with ducks and geese is evidence these groups may be more closely related to each other than either is to storks.
Parasitism is part of one explanation for the evolution of secondary sex characteristics seen in breeding males throughout the animal world, such as the plumage of male peacocks and manes of male lions. According to this theory, female hosts select males for breeding based on such characteristics because they indicate resistance to parasites and other disease.

[edit] Co-speciation

In rare cases, a parasite may even undergo co-speciation with its host. One particularly remarkable example of co-speciation exists between the simian foamy virus (SFV) and its primate hosts. In one study, the phylogenies of SFV polymerase and the mitochondrial cytochrome oxidase subunit II from African and Asian primates were compared.^[13] Surprisingly, the phylogenetic trees were very congruent in branching order and divergence times. Thus, the simian foamy viruses may have co-speciated with Old World primates for at least 30 million years.