Today, I learned that biologists use cladistics rather than taxonomy
https://www.tiktok.com/t/ZP8rLJcgY/
Taxonomy is a field of study: how should we classify things? Cladistics is a method using trees to classify things. Hence the confusion, I think. They are not mutually exclusive but often overlap.
Phylogenetic trees tend to be based on similarities in either token sequences (as in ribosomal 16S rRNA for the first ones) or overall genomic similarity. This is in contrast to more traditional measurements (ask an entomologist how they know a beetle is species X versus Y, and they will usually describe a morphological key: if this leg segment is longer, it is in this branch; next, look at the number of spots, etc.).
Genetics is really tricky, though, because A) most organisms are unicellular and can share genes horizontally, making a stable tree really hard. And B) there are many ways to measure genetic distance, and no good way to know if one method is generally “better” than another. As a fun game, imagine how many sequences you could make from 10 heads and 10 tails. Raw counts of all sequences are 10 and 10. But some sequences will be closer than others (10H 10T is close to 9H 1T, 9T 1H, but the two reverses are farther from each other). Each base position can be considered an independent dimension, and high-dimensional distance metrics become unusual.
Taxonomy is a broad term for sorting things into hierarchical categories. It is not just used in biology.
Phylogenetics is the study of evolutionary relationships. We sort organisms into categories based on their evolutionary relationships. Because we are sorting them into categories, it is taxonomy.
Cladistics is a specific approach to phylogenetics where organisms are grouped into “clades.” All organisms in a clade must have common ancestry, and a true clade would include every organism that shares that ancestry. Dolphins, dogs, and salmon are all part of the clade that includes all vertebrates. Dolphins and dogs are part of the mammal clade, but salmon are excluded from it, because the most recent common ancestor of dogs and dolphins is more recent. Salmon diverged much earlier on the tree.
When we create cladograms we do include genetic data
