Which genes or proteins to compare in a phylogenetic tree?

Question

[crawforc3]

I am a student and I have a fun problem: My friend doesn't like cats and thinks raccoon's are "way cooler." I want to build a phylogenetic tree and show him that we're more closely related to cats and therefore cats are cooler.

However, my school assignments always told me which gene or protein to use for analyses.

So how do I decide which gene/prot to compare without looking back at old assignments?

I'll be looking at house pets so I know I need something that cats, dogs, lizards, gold fish, and snakes have in common.

What should be my next steps?

Answer 1

[Jean-Karim Heriche]

Phylogenies using a single gene are not reliable. For this kind of comparison, you should probably use fast evolving genes such as mitochondrial genes. Check the literature, people have most likely already worked out which genes to use and how.

[crawforc3]

Why faster evolving genes? Would that make a more apparent differentiation?

[Jean-Karim Heriche]

Because you're interested in species which diverged relatively recently i.e. their most recent common ancestors are not old so faster evolving sequences will contain more information.