Using uniform priors for root calibration and enforcing monophyly

[Daniel Eusebio Quintero Vallejo]

Dear all,

I’m working on a time-calibrated phylogenetic analysis using BEAST, and I’d appreciate your advice on a couple of calibration strategies I’ve implemented:

1. I used a uniform prior on the root node to prevent unrealistically old divergence times. The minimum value is based on a reliable fossil (crown group), and the maximum corresponds to the age of the closest ingroup calibration, ensuring consistency with the other fossil constraints.

2. I also applied a uniform prior to a specific node to enforce the monophyly of a well-supported clade. This was done by setting bounds that match the surrounding calibrations. The aim is not to calibrate that node per se, but rather to constrain topology based on strong independent evidence of monophyly (molecular, morphological, and previous studies).

Is this approach considered appropriate? This is an strategy that I've heard from my classes. Moreover, I'm being congruent with other assumptions related to the other calibrations. 

Additionally, I’d be very grateful if anyone could recommend references or published studies where uniform priors are used for similar purposes (root calibration or monophyly constraints). So far, I’ve found little explicit justification in the literature.

Thanks in advance for your help and suggestions!

Best,
Daniel