Re: [dinosaur] Fossil theropods, dated phylogenies: topology, divergence dates, and macroevolutionary inferences

["David Marjanovic" <david.marjanovic@gmx.at>]

> This is a good paper for what it is about, namely showing the difference
> between different software packages and algorithms within them in trying
> to assess the same question. But please don't go to this for details on
> theropod systematics!

Having been a reviewer on that paper* twice, I agree, and I'm sure so do the 
authors: this is a methods paper that has nothing to say about the validity of 
*Wellnhoferia* in particular or about individual/sexual/ontogenetic variation 
in general, so I didn't even bring these topics up in my review.

In a work on phylogeny, or on topics that require a phylogeny (diversification 
rates, radiations into morphospace, phylogeography etc. etc.), it wouldn't even 
be appropriate to just grab two published matrices, take them for granted and 
run analyses on them. They're two different matrices, so they're probably both 
incomplete and both wrong! :-) The thing to do would be to compare the matrices 
to each other, to the descriptive literature and to specimens** to find and 
correct the mistakes in the scoring and the coding, to merge them and to run a 
new phylogenetic analysis (or several) on the merged matrix. (In the course of 
_such_ work, questions of individual/sexual/ontogenetic variation would of 
course become _very_ important.***) But that is unnecessary (and of course way 
too much work) for the purposes of Bapst et al. (2016).

* Although the paper doesn't mention any reviewers, I don't think I'm revealing 
any secrets here – I signed my review as usual. Between the first and the 
second round, the journal became double-blind, so I didn't see the authors' 
names the second time; but it still doesn't say reviewers shouldn't identify 
themselves if they so choose.
** As I've done with one matrix here: 
https://urldefense.proofpoint.com/v2/url?u=https-3A__peerj.com_preprints_1596_&d=DQIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=yqnFSMdyFp4w0F04C3cZF3sfcRMlQ2P9CblBwB9ySZc&s=pK_E_bboxe57gj7L0GB5WzGhCG2TQ6oDVZuLuBf-PR0&e=
  – expect a second version within the next few weeks. Note that the confusion 
over different versions of the matrix of Ruta & Coates (2007) has evaporated: a 
few characters were simply labeled wrong in the first file I had of that 
matrix, there is only one version.
*** Wiens JJ, Bonett RM, Chippindale PT (2005) Ontogeny discombobulates 
phylogeny: paedomorphosis and higher-level salamander relationships. Systematic 
Biology 54: 91–110. Open access: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__sysbio.oxfordjournals.org_content_54_1_91.full&d=DQIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=yqnFSMdyFp4w0F04C3cZF3sfcRMlQ2P9CblBwB9ySZc&s=VsXYau5xLoIoqcL38-NmzWm8cg64Dm6qRfQ6ek7Af7A&e=