Cladistics - Phylogenetics

Phylogenetics

The outcome of a cladistic analysis is a cladogram – a tree-shaped diagram (dendrogram) that represents a phylogenetic hypothesis, a hypothesis on evolutionary relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now very commonly used in phylogenetic analysis.

Every cladogram is based on a particular dataset that was analyzed with a particular method. Datasets are tables consisting of molecular, morphological, ethological and/or other characters and a list of operational taxonomic units (OTUs) which may be genes, individuals, populations, species, or larger taxa that are presumed to be monophyletic and that are presumed to form, all together, one large clade; phylogenetic analysis reconstructs the branching pattern within that clade. Different datasets and different methods, not to mention violations of the mentioned assumptions, often result in different cladograms. Only scientific investigation can show which is more likely to be correct.

Until recently, for example, cladograms like the following have generally been accepted as accurate representations of the ancestral relations among turtles, lizards, crocodilians, and birds:

If this phylogenetic hypothesis is correct, the last common ancestor of turtles and birds, at the ⊣ connection near the ▼ (a ⊤ in some browsers) lived earlier than the last common ancestor of lizards and birds, near the ♦. Most molecular evidence, however, produces cladograms more like this:

If this is accurate, the last common ancestor of turtles and birds lived later than the last common ancestor of lizards and birds. Since the cladograms provide competing accounts of real events, at most one of them is correct.