Simulic
English

Cladograms and phylogenetic trees – build them from characters or sequences

BiologyEvolutionAges 17–18

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Build a cladogram from a table of shared derived characters rooted with an outgroup, or from aligned DNA and protein sequences: count the differences, join the closest pair step by step and compare your tree with the accepted one. A molecular clock turns differences into divergence times; show the tree on the three domains and test whether traditional groups are monophyletic, paraphyletic or polyphyletic.

Lesson: Evidence for evolution: cladograms, phylogenetic trees and the molecular clock

What it shows

A cladogram groups organisms by shared derived characters: features that appeared in a common ancestor and were passed on to all its descendants. The outgroup shows the ancestral state, so it roots the tree. Molecular data work the same way: species whose DNA or protein sequences differ least share the most recent common ancestor. Here you build trees both ways, from a character matrix and from simulated aligned sequences, then compare them with the accepted tree. A molecular clock calibrated with a fossil date converts differences into divergence times, and traditional groups such as reptiles or prokaryotes can be tested against the tree.

How to use

Choose a Dataset. For characters, tap a cell to switch 0 and 1, untick a column to drop a character, or change the Outgroup; switch between Cladogram and Nested sets. For sequences, set the length, then tap the smallest number in the difference table, or press Join the closest pair, until the tree is complete. Tick Compare with the accepted tree, choose a calibration for the molecular clock and pick a Group to test.

Parameters you can change

  • Dataset Vertebrates (characters), Plants (characters), Primates (DNA sequences), Vertebrates (protein), Three domains (rRNA sequences)
  • Sequence length 20–1000 sites
  • Show the accepted tree for comparison

Questions to explore

  1. Why do you need an outgroup to decide which state of a character is derived?
  2. Why do trees built from short sequences sometimes differ from the accepted tree?
  3. Why are prokaryotes not a clade on the three-domain tree of life?

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