Indicating co-PI status on a paper Authorship order in life sciences is intricate and has many problems. By convention, order is by the amount of contribution (decreasing). Also by convention, the PI/supervisor/"senior author" appears last. Things start getting complicated when you have many contributors.

I would like to focus on the end of the author list. When there are several PIs, they all appear at the end. However, if you consider the before-last author, a reader would not be able to know whether this is the author with the least contribution or alternatively a co-PI. I have seen different "solutions" to this problem (e.g. marking all senior authors as corresponding authors).

I would like to know what kind of solutions you have seen for this problem, and whether these solutions are recognized by institutions and funding agencies.

For those of you wondering why these intricacies matter - authorship order can play an important role in getting a faculty position, awards, grants and tenure. For example, for some fellowships you may only list publications for which you are the first author.
Actually, I've never seen a paper where co-principal investigators (with respect to a grant) have been distinguished—and I was co-advised as a graduate student in exactly such a circumstance.

However, I don't think this is as big a problem as you think. If you were a co-PI, you would indicate the corresponding grant as part of your CV, as well as the resulting publications. So it shouldn't be too hard to figure out who contributed what.

Also, in my own circumstance, I am actively co-advising several students at the moment. In these collaborations, we assign the "senior author" position to the most "relevant" author for the publication. For instance, I'm in engineering and one of my collaborators is in CS. When we publish in a CS venue, he's the senior author; when we publish in an engineering venue, I'm the senior author.

If it's really important, though, to indicate the co-PI issue, you could mention this in the acknowledgments section, since that's where you'd list the grant support in any case. You could write something like


  F.O.O. and B.A.R. were co-principal investigators on grant XYZ from funding agency ABC.


or whatever comparable wording satisfies your needs as well as those of the funding agencies.