Evolutionary processes may make it difficult to infer phylogenetic relationships. For example, shared derived character states may be erased by subsequent evolution, as when successive base pair substitutions occur at the same site in a DNA sequence. If multiple lineages originate from a common ancestor within a short time, the relationships among them may be unresolved because there was not enough time for derived character states to evolve between successive branching events. An accurately estimated phylogeny of genes (DNA sequences) from different species may differ from the phylogeny of the species themselves. With enough data, these difficulties can usually be surmounted.

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