Mapping NCBI taxID to evolution time?

Question

[johnnytam100]

I want to map NCBI taxID to their evolution time. Do we have a database for such correlation?

Answer 1

[Michael]

I assume you mean divergence time of multiple taxa because evolution is a process. Also, the taxonomy is not a phylogeny. Look at TimeTree of Life: http://www.timetree.org/ There you can enter two tax ids and get estimates of their divergence times from the literature, or an evolutionary timeline for a single taxon.

[johnnytam100]

Thank you for the suggestion! I have download a .nwk file from them now. Do you know how can I convert the tree to the divergence times of different clades? Btw, I will be grateful if you can suggest a concise book so I can clarify my concepts (e.g. taxonomy vs phylogeny, evolution time etc.)

[Michael]

Download the image file as well, then it will become more clear. The branching times are given in Mya (million years ago) in the Newick tree.

Example for "Crustacea". The root of the tree is put at ~530Mya (the last common ancestor of all crustaceans), Ostracoda and Malacostraca diverged 512 Mya, and so on

((Ostracoda:512.26378820,Malacostraca:512.26378820)'7':17.73621180,(((Remipedia:413.84600000,Cephalocarida:413.84600000)'6':88.55274300,Branchiopoda:502.39874300)'14':27.60125700,Maxillopoda:530.00000000)'12':0.00000000);

[Michael]

As an introductory textbook try this:

Lemey, P., Salemi, M., & Vandamme, A. (Eds.). (2009). The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (2nd ed.). Cambridge: Cambridge University Press. doi:10.1017/CBO9780511819049 https://doi.org/10.1017/CBO9780511819049