[Hurinthalion (OP)]

'When' would you use nucleotides (or any other molecular data) instead of amino acids to construct phylogenetic trees?

[evan_au]

You might use protein amino-acid sequences when:
- Temperatures are so high that fossil DNA has been corrupted beyond our ability to read, but there is some intact protein available.
- When you are looking for functional changes in a protein, rather than non-functional genetic changes in the protein.
- But untangling and reading the sequence of a protein is not easy, and different techniques need to be developed for every different protein

In most cases, if you can recover intact DNA, you would use it, because:
- You can read the sequence of every protein in the same way, without having to develop a new technique for every protein
- You can read changes in "non-protein-coding" DNA, which often changes more rapidly than protein-coding segments, allowing the researcher to chart even very close family relationships
- Techniques for reading DNA have accelerated exponentially over the past few decades, making it the cheapest and fastest method available
- COVID-19 has resulted in the deployment of far more PCR machines and DNA sequencers than ever before...
- If you can't read nuclear DNA, mitochondrial DNA will also give some clues (there are more copies of mitochondrial DNA in each cell than nuclear DNA)