Maximum Parsimony (phylogenetics) - in Detail

In Detail

Parsimony is part of a class of character-based tree estimation methods which use a matrix of discrete phylogenetic characters to infer one or more optimal phylogenetic trees for a set of taxa, commonly a set of species or reproductively isolated populations of a single species. These methods operate by evaluating candidate phylogenetic trees according to an explicit optimality criterion; the tree with the most favorable score is taken as the best estimate of the phylogenetic relationships of the included taxa. Maximum parsimony is used with most kinds of phylogenetic data; until recently, it was the only widely used character-based tree estimation method used for morphological data.

Estimating phylogenies is not a trivial problem. A huge number of possible phylogenetic trees exist for any reasonably sized set of taxa; for example, a mere ten species gives over two million possible unrooted trees. These possibilities must be searched to find a tree that best fits the data according to the optimality criterion. However, the data themselves do not lead to a simple, arithmetic solution to the problem. Ideally, we would expect the distribution of whatever evolutionary characters (such as phenotypic traits or alleles) to directly follow the branching pattern of evolution. Thus we could say that if two organisms possess a shared character, they should be more closely related to each other than to a third organism that lacks this character (provided that character was not present in the last common ancestor of all three, in which case it would be a symplesiomorphy). We would predict that bats and monkeys are more closely related to each other than either is to a fish, because they both possess hair—a synapomorphy. However, we cannot say that bats and monkeys are more closely related to one another than they are to whales because they share hair, because we believe the last common ancestor of the three had hair.

However, the phenomena of convergent evolution, parallel evolution, and evolutionary reversals (collectively termed homoplasy) add an unpleasant wrinkle to the problem of estimating phylogeny. For a number of reasons, two organisms can possess a trait not present in their last common ancestor: If we naively took the presence of this trait as evidence of a relationship, we would reconstruct an incorrect tree. Real phylogenetic data include substantial homoplasy, with different parts of the data suggesting sometimes very different relationships. Methods used to estimate phylogenetic trees are explicitly intended to resolve the conflict within the data by picking the phylogenetic tree that is the best fit to all the data overall, accepting that some data simply will not fit. It is often mistakenly believed that parsimony assumes that convergence is rare; in fact, even convergently derived characters have some value in maximum-parsimony-based phylogenetic analyses, and the prevalence of convergence does not systematically affect the outcome of parsimony-based methods.

Data that do not fit a tree perfectly are not simply "noise", they can contain relevant phylogenetic signal in some parts of a tree, even if they conflict with the tree overall. In the whale example given above, the lack of hair in whales is homoplastic: It reflects a return to the condition present in ancient ancestors of mammals, who lacked hair. This similarity between whales and ancient mammal ancestors is in conflict with the tree we accept, since it implies that the mammals with hair should form a group excluding whales. However, among the whales, the reversal to hairlessness actually correctly associates the various types of whales (including dolphins and porpoises) into the group Cetacea. Still, the determination of the best-fitting tree—and thus which data do not fit the tree—is a complex process. Maximum parsimony is one method developed to do this.

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