MPTP vs PTP vs ABGD

[tej...@gmail.com]

Dear authors, dear groupies.

I've run some species delimitation analyses on your web pages, both PTP and MPTP, and analyses yielded diverting results. While PTP supported 36 species, MPTP supported only 20 MOTUs. Moreover, one of the MPTP MOTUs was even paraphyletic. Interestingly, the third method, ABGD, gave 34 species.

Similarly, a month ago, I've run an analysis on ca 400 COI amphipod sequences. The story was somewhat similar. PTP and ABGD yielded similar results, with 169 and 162 MOTUs, respectively. At the same time MPTP gave really low number of MOTUs. If I remeber correctly, only 35 species. Of course, this result was rebuted as it lumped together species from different parts of Europe, and I am dealing with narrowly distributed subterranean amphipods (on genus level), or morphologically differint species.

I wonder if there is any consensus what kind of dataset should be used with MPTP, like smaller, closely related species groups or something similar?

Thank you for any help,

cheers,

Teo 

[Alexandros Stamatakis]

Dear Teo,

> I've run some species delimitation analyses on your web pages, both PTP
> and MPTP, and analyses yielded diverting results. While PTP supported 36
> species, MPTP supported only 20 MOTUs. Moreover, one of the MPTP MOTUs
> was even paraphyletic.

This can not be as they are strictly defined on the input tree you
provide, so either a subtree of the phylogeny is a single species or it
contains several species, so I don't see how this can be paraphyletic.

> Interestingly, the third method, ABGD, gave 34
> species.

As far as I understand ABGD is higly sensitive to the parameters you
pass to it.

> Similarly, a month ago, I've run an analysis on ca 400 COI amphipod
> sequences. The story was somewhat similar. PTP and ABGD yielded similar
> results, with 169 and 162 MOTUs, respectively. At the same time MPTP
> gave really low number of MOTUs. If I remeber correctly, only 35
> species.

Did you check the MCMC convergence?

> Of course, this result was rebuted as it lumped together
> species from different parts of Europe, and I am dealing with narrowly
> distributed subterranean amphipods (on genus level), or morphologically
> differint species.
> I wonder if there is any consensus what kind of dataset should be used
> with MPTP, like smaller, closely related species groups or something
> similar?

It's hard to tell as we don't know the ground truth really. In
principle, just from a purely mathematical point of view, I would tend
to trust the mptp results more. It would be nice if you could share the
trees with us that generated these results, after all the only parameter
influencing the results of ptp and mptp are the tree shape and branch
lengths.

Alexis

> Thank you for any help,
> cheers,
> Teo
>

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Christopher Blair]

Hi Teo, 

I assume you read our MER paper comparing these methods? In our data, PTP yielded an unrealistically high number of species. There were similar issues with mGMYC, whereas the single threshold GMYC tended to lump everything. In our case, mPTP and ABGD were concordant and the results did not change much with different data set characteristics. With that said, based on my experience mPTP does tend to be conservative with species estimates. However, one could argue that this is a good thing. 

Best wishes, 

Chris

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