Maximum Parsimony (phylogenetics) - Character Data

Character Data

The input data used in a maximum parsimony analysis is in the form of "characters" for a range of taxa. There is no generally agreed-upon definition of a phylogenetic character, but operationally a character can be thought of as an attribute, an axis along which taxa are observed to vary. These attributes can be physical (morphological), molecular, genetic, physiological, or behavioral. The only widespread agreement on characters seems to be that variation used for character analysis should reflect heritable variation. Whether it must be directly heritable, or whether indirect inheritance (e.g., learned behaviors) is acceptable, is not entirely resolved.

Each character is divided into discrete character states, into which the variations observed are classified. Character states are often formulated as descriptors, describing the condition of the character substrate. For example, the character "eye color" might have the states "blue" and "brown." Characters can have two or more states (they can have only one, but these characters lend nothing to a maximum parsimony analysis, and are often excluded).

Coding characters for phylogenetic analysis is not an exact science, and there are numerous complicating issues. Typically, taxa are scored with the same state if they are more similar to one another in that particular attribute than each is to taxa scored with a different state. This is not straightforward when character states are not clearly delineated or when they fail to capture all of the possible variation in a character. How would one score the previously mentioned character for a taxon (or individual) with hazel eyes? Or green? As noted above, character coding is generally based on similarity: Hazel and green eyes might be lumped with blue because they are more similar to that color (being light), and the character could be then recoded as "eye color: light; dark." Alternatively, there can be multi-state characters, such as "eye color: brown; hazel, blue; green."

Ambiguities in character state delineation and scoring can be a major source of confusion, dispute, and error in phylogenetic analysis using character data. Note that, in the above example, "eyes: present; absent" is also a possible character, which creates issues because "eye color" is not applicable if eyes are not present. For such situations, a "?" ("unknown") is scored, although sometimes "X" or "-" (the latter usually in sequence data) are used to distinguish cases where a character cannot be scored from a case where the state is simply unknown. Current implementations of maximum parsimony generally treat unknown values in the same manner: the reasons the data are unknown have no particular effect on analysis. Effectively, the program treats a ? as if it held the state that would involve the fewest extra steps in the tree (see below), although this is not an explicit step in the algorithm.

Genetic data are particularly amenable to character-based phylogenetic methods such as maximum parsimony because protein and nucleotide sequences are naturally discrete: A particular position in a nucleotide sequence can be either adenine, cytosine, guanine, or thymine / uracil, or a sequence gap; a position (residue) in a protein sequence will be one of the basic amino acids or a sequence gap. Thus, character scoring is rarely ambiguous, except in cases where sequencing methods fail to produce a definitive assignment for a particular sequence position. Sequence gaps are sometimes treated as characters, although there is no consensus on how they should be coded.

Characters can be treated as unordered or ordered. For a binary (two-state) character, this makes little difference. For a multi-state character, unordered characters can be thought of as having an equal "cost" (in terms of number of "evolutionary events") to change from any one state to any other; complementarily, they do not require passing through intermediate states. Ordered characters have a particular sequence in which the states must occur through evolution, such that going between some states requires passing through an intermediate. This can be thought of complementarily as having different costs to pass between different pairs of states. In the eye-color example above, it is possible to leave it unordered, which imposes the same evolutionary "cost" to go from brown-blue, green-blue, green-hazel, etc. Alternatively, it could be ordered brown-hazel-green-blue; this would normally imply that it would cost two evolutionary events to go from brown-green, three from brown-blue, but only one from brown-hazel. This can also be thought of as requiring eyes to evolve through a "hazel stage" to get from brown to green, and a "green stage" to get from hazel to blue, etc.

There is a lively debate on the utility and appropriateness of character ordering, but no consensus. Some authorities order characters when there is a clear logical, ontogenetic, or evolutionary transition among the states (for example, "legs: short; medium; long"). Some accept only some of these criteria. Some run an unordered analysis, and order characters that show a clear order of transition in the resulting tree (which practice might be accused of circular reasoning). Some authorities refuse to order characters at all, suggesting that it biases an analysis to require evolutionary transitions to follow a particular path.

It is also possible to apply differential weighting to individual characters. This is usually done relative to a "cost" of 1. Thus, some characters might be seen as more likely to reflect the true evolutionary relationships among taxa, and thus they might be weighted at a value 2 or more; changes in these characters would then count as two evolutionary "steps" rather than one when calculating tree scores (see below). There has been much discussion in the past about character weighting. Most authorities now weight all characters equally, although exceptions are common. For example, allele frequency data is sometimes pooled in bins and scored as an ordered character. In these cases, the character itself is often downweighted so that small changes in allele frequencies count less than major changes in other characters. Also, the third codon position in a coding nucleotide sequence is particularly labile, and is sometimes downweighted, or given a weight of 0, on the assumption that it is more likely to exhibit homoplasy. In some cases, repeated analyses are run, with characters reweighted in inverse proportion to the degree of homoplasy discovered in the previous analysis (termed successive weighting); this is another technique that might be considered circular reasoning.

Character state changes can also be weighted individually. This is often done for nucleotide sequence data; it has been empirically determined that certain base changes (A-C, A-T, G-C, G-T, and the reverse changes) occur much less often than others. These changes are therefore often weighted more. As shown above in the discussion of character ordering, ordered characters can be thought of as a form of character state weighting.

Some systematists prefer to exclude characters known to be, or suspected to be, highly homoplastic or that have a large number of unknown entries ("?"). As noted below, theoretical and simulation work has demonstrated that this is likely to sacrifice accuracy rather than improve it. This is also the case with characters that are variable in the terminal taxa: theoretical, congruence, and simulation studies have all demonstrated that such polymorphic characters contain significant phylogenetic information.