How does maximum parsimony select a phylogenetic tree?

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Maximum parsimony methods select a phylogenetic tree by identifying the evolutionary path that requires the fewest total number of character changes across all branches. By minimizing these transitions, the method operates on the assumption that the shortest evolutionary path is the most probable explanation for the observed diversity among species.12

When reconstructing these trees, researchers map character states—such as DNA sequences or morphological traits—onto potential tree structures. The tree that accounts for all data with the minimum number of changes is considered the most parsimonious. In cases where certain changes are known to be more likely than others, such as transitions versus transversions in nucleotide bases, parsimony methods can be adjusted to account for these varying probabilities.12

While this approach is a standard tool in cladistics, it is important to note that the most parsimonious path is not always the actual historical path, as evolution may involve independent, parallel, or intermediate changes that do not follow a strictly minimal route.12