Parallel vs. convergent evolution
For a particular trait, proceeding in each of two lineages from a specified ancestor to a later descendant, parallel and convergent evolutionary trends can be strictly defined and clearly distinguished from one another. However the cutoff point for what is considered convergent and what is considered parallel evolution is assigned somewhat arbitrarily. When two species are similar in a particular character, evolution is defined as parallel if the ancestors were also similar and convergent if they were not. However, this definition is somewhat murky. All organisms share a common ancestor more or less recently, so the question of how far back to look in evolutionary time and how similar the ancestors need to be for one to consider parallel evolution to have taken place is not entirely resolved within evolutionary biology. Some scientists have argued parallel evolution and convergent evolution are more or less indistinguishable from one another. Others have argued that we should not shy away from the gray area and that there are still important distinctions between parallel and convergent evolution.
When the ancestral forms are unspecified or unknown, or the range of traits considered is not clearly specified, the distinction between parallel and convergent evolution becomes more subjective. For instance, the striking example of similar placental and marsupial forms is described by Richard Dawkins in The Blind Watchmaker as a case of convergent evolution, because mammals on each continent had a long evolutionary history prior to the extinction of the dinosaurs under which to accumulate relevant differences. Stephen Jay Gould describes many of the same examples as parallel evolution starting from the common ancestor of all marsupials and placentals. Many evolved similarities can be described in concept as parallel evolution from a remote ancestor, with the exception of those where quite different structures are co-opted to a similar function. For example, consider Mixotricha paradoxa, a eukaryotic microbe which has assembled a system of rows of apparent cilia and basal bodies closely resembling that of ciliates but which are actually smaller symbiont microorganisms, or the differently oriented tails of fish and whales. Conversely, any case in which lineages do not evolve together at the same time in the same ecospace might be described as convergent evolution at some point in time.
The definition of a trait is crucial in deciding whether a change is seen as divergent, or as parallel or convergent. In the image above, note that since serine and threonine possess similar structures with an alcohol side chain, the example marked "divergent" would be termed "parallel" if the amino acids were grouped by similarity instead of being considered individually. As another example, if genes in two species independently become restricted to the same region of the animals through regulation by a certain transcription factor, this may be described as a case of parallel evolution - but examination of the actual DNA sequence will probably show only divergent changes in individual basepair positions, since a new transcription factor binding site can be added in a wide range of places within the gene with similar effect.
A similar situation occurs considering the homology of morphological structures. For example, many insects possess two pairs of flying wings. In beetles, the first pair of wings is hardened into wing covers with little role in flight, while in flies the second pair of wings is condensed into small halteres used for balance. If the two pairs of wings are considered as interchangeable, homologous structures, this may be described as a parallel reduction in the number of wings, but otherwise the two changes are each divergent changes in one pair of wings.
Similar to convergent evolution, evolutionary relay describes how independent species acquire similar characteristics through their evolution in similar ecosystems, but not at the same time (dorsal fins of sharks and ichthyosaurs).
Defined as the repeated independent evolution of the same reproductive isolating mechanism (Schluter and Nagel 1995). An example of this may occur when a species colonizes several new areas which are isolated from, but environmentally similar to, each other. Similar selective pressures in these environments result in parallel evolution among the traits that confer reproductive isolation.
- Coloration that serves as a warning to predators and for mating displays has evolved in many different species.
- In the plant kingdom, the most familiar examples of parallel evolution are the forms of leaves, where very similar patterns have appeared again and again in separate genera and families.
- In Arabidopsis thaliana it has been suggested that populations adapt to local climate through parallel evolution 
- In butterflies, many close similarities are found in the patterns of wing colouration, both within and between families.
- Old and New world porcupines shared a common ancestor, both evolved strikingly similar quill structures; this is also an example of convergent evolution as similar structures evolved in hedgehogs, echidnas and tenrecs.
- Contemporaneous evolution of the extinct browsing-horses and extinct paleotheres both of which shared the same environmental space.
- Some extinct Archosaurs evolved an upright posture and likely were warm-blooded. These two characteristics are also found in most mammals. Interestingly, modern crocodiles have a four chambered heart and a crurotarsal, the latter being also a characteristic of therian mammals.
- The extinct pterosaurs and the birds both evolved wings as well as a distinct beak, but not from a recent common ancestor.
- Internal fertilization has evolved independently in sharks, some amphibians and amniotes.
- The Patagium is a fleshy membrane that is found in gliding mammals such as: flying lemurs, flying squirrels, sugar gliders and the extinct Volaticotherium. These mammals acquired the patagium independently.
- Pyrotherians have evolved a body plan similar to proboscideans.
- The eye of the octopus has the same complicated structure as the human eye. As a result, it is often substituted in studies of the eye when using a human eye would be inappropriate. As the two species diverged at the time animals evolved into vertebrates and invertebrates this is extraordinary.
- Certain arboreal frog species, 'flying' frogs, in both Old World families and New World families have developed the ability of gliding flight. They have "enlarged hands and feet, full webbing between all fingers and toes, lateral skin flaps on the arms and legs, and reduced weight per snout-vent length". 
Parallel evolution between marsupials and placentals
One of the most spectacular examples of parallel evolution is provided by the two main branches of the mammals, the placentals and marsupials, which have followed independent evolutionary pathways following the break-up of land-masses such as Gondwanaland roughly 100 million years ago. In South America, marsupials and placentals shared the ecosystem (prior to the Great American Interchange); in Australia, marsupials prevailed; and in the Old World the placentals won out. However, in all these localities mammals were small and filled only limited places in the ecosystem until the mass extinction of dinosaurs sixty-five million years ago. At this time, mammals on all three landmasses began to take on a much wider variety of forms and roles. While some forms were unique to each environment, surprisingly similar animals have often emerged in two or three of the separated continents. Examples of these include the litopterns and horses, whose legs are difficult to distinguish; the European sabre-toothed cat (Machairodontinae) and the South American marsupial sabre-tooth (Thylacosmilus); the Tasmanian wolf and the European wolf; likewise marsupial and placental moles, flying squirrels, and (arguably) mice.
- Parallel evolution: Online Biology Glossary
- Zhang, J. and Kumar, S. 1997. Detection of convergent and parallel evolution at the amino acid sequence level. Mol. Biol. Evol. 14, 527-36.
- ARENDT, J; REZNICK, D (January 2008). "Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?". Trends in Ecology & Evolution 23 (1): 26–32. doi:10.1016/j.tree.2007.09.011.
- Pearce, T. (10 November 2011). "Convergence and Parallelism in Evolution: A Neo-Gouldian Account". The British Journal for the Philosophy of Science 63 (2): 429–448. doi:10.1093/bjps/axr046.
- Stearns, F. W. and C. B. Fenster (2013). Evidence for parallel adaptation across the natural range of Arabidopsis thaliana. Ecology & Evolution. http://onlinelibrary.wiley.com/doi/10.1002/ece3.622/full
- Emerson, S.B., & Koehl, M.A.R. (1990). "The interaction of behavioral and morphological change in the evolution of a novel locomotor type: 'Flying' frogs." Evolution, 44(8), 1931-1946
- Dawkins, R. 1986. The Blind Watchmaker. Norton & Company.
- Mayr. 1997. What is Biology. Harvard University Press
- Schluter, D., E. A. Clifford, M. Nemethy, and J. S. McKinnon. 2004. Parallel evolution and inheritance of quantitative traits. American Naturalist 163: 809–822.
- McGhee, G.R. 2011. Convergent Evolution: Limited Forms Most Beautiful. Vienna Series in Theoretical Biology, Massachusetts Institute of Technology Press, Cambridge (MA). 322 pp.