Limitations of Molecular Systematics
Molecular systematics is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be monophyletic.
Molecular phylogenies are sensitive to the assumptions and models that go into making them. They face problems like long-branch attraction, saturation, and taxon sampling problems: This means that strikingly different results can be obtained by applying different models to the same dataset.
Read more about this topic: Molecular Phylogenetics
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