Dear all. In recent, i try to extract the taxon age from a phylogeny tree(time-calibrated) and get the divergence time of each species, but i searched many websites and can not found a function that can do this work. Is there any specific package that can do this work? Thanks
Check out this answer on phytools: http://blog.phytools.org/2013/10/finding-edge-lengths-of-all-terminal.html
Dear Sun Lu thank you for asking the very interesting technical question. The following links might be useful in your analysis:
https://taming-the-beast.org/tutorials/FBD-tutorial/FBD-tutorial.pdf
https://groups.google.com/g/beast-users?pli=1
and
TimeTree: A Resource for Timelines, Timetrees, and Divergence Times
https://academic.oup.com/mbe/article/34/7/1812/3091705
Also please have a look at the answers given to the following closely related question which has been asked earlier on RG:
How can I measure or determine the age of the species when I use a constructed phylogenetics tree?
https://www.researchgate.net/post/How-can-I-measure-or-determine-the-age-of-the-species-when-I-use-a-constructed-phylogenetics-tree
Unfortunately this interesting question has received only two answers.
Good luck with your work and please stay safe and healthy!
It is not possible to extract taxon age from phylogeny. Phylogeny is just relationship. It has no inherent age. There are two principle methods for estimating clade age. Most popular is to convert molecular divergence into a time scale. This is usually done using fossils to calibrate the rate. Since fossils are only minimum ages, the resulting molecular estimate is also a minimum. But this is often ignored or various manipulations (e.g. priors) are introduced to give the appearance of empirical evidence of upper age limits. The other method is tectonic correlation - where allopatric clades have boundaries corresponding to tectonic structures (e.g. transform faults, subduction zones, spreading ridges etc). this gives an estimate of an actual age, but is contingent upon various factors such as the role of tectonic reactivation, duration of the tectonic event, and accuracy of geological dating.
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