I wonder if someone could tell me if the conclusions in
that the bacterial flagellum is shown as ancestral to the type three secretory system is the latest word on the issue? Apologies if this paper has been discussed previously. I’ll explain my reason for asking in comments if anyone is curious.
Yes it’s a point creationists typically bring up under the misapprehension that this somehow disproves that flagella evolved from type III secretion systems.
Notice that it says the “non-flagellar type III secretion system”. Technically there is no such thing as “the” T3SS, there are lots of different ones. And if one infers a phylogeny from the sequences of the genes incoding those T3SSs, of those carrying T3SSs that aren’t part of flagella, you find that those T3SSs derive from flagella, obviously through some sort of loss of flagellar components.
That doesn’t mean flagella didn’t initially pass through a stage in it’s evolution that was of the same complexity and function as those non-flagellar T3SSs. After all, the flagellum has a T3SS-like structure as part of it, and without which it could not be assembled and function. Those flagellar T3SSs are in fact responsible for transporting extracellular flagella components across the membrane and outside of the cell. When flagella are assembled, a flagellar T3SS is assembled first and then starts functioning as a secretion system in order to build up further into the flagellum.
So all this really means is that the organisms that had reached the “secretion system stage” in the evolution of flagella, didn’t leave any descendants that survived until the present day and stayed at that level of complexity. If any stayed at that level of complexity, they either went extinct or we haven’t found them.
So the inference that flagella passed through such a stage in their evolution can’t be supported by any presently known phylogeny, and must therefore rest on other pieces of evidence (such as flagellar assembly order and the functions of it’s subcomponents).
I found two previous mentions, one of which has useful discussion. See the first comment following, by @Rumraket of course. 
I’ll explain my reason for asking in comments if anyone is curious.
If you hadn’t written that, I might not be curious. But you did! 
Much appreciated, Mikkel
No problemo.
On a related note I just discovered the link to Matzke’s original (and updated in 2006) 2003 article on the flagellum no longer works, and can now apparently only be found by accessing the wayback machine here: Evolution of the bacterial flagellum
Thanks, Dan. I will read through and digest! Some time ago, I joined a Facebook group at the behest of Denyse O’Leary, but never went anywhere with it. I dipped back in due to the untimely demise of Günter Bechly. I left a drive-by comment and got dragged in.
Yes, I know very well how that can happen. It’s only happened to me once this week, maybe twice, and it’s still Tuesday. 
Is this review paper a reasonable source?
https://www.annualreviews.org/content/journals/10.1146/annurev-micro-032521-025503
I see Nick Matzke doesn’t get a mention among the 130 citations, whereas the 2012 paper by Abby, Rocha is no 1.
Yes. What I particularly like about it is that they distinguish between the injectisome and the T3SS (they make this very clear in the beginning of part 3), and don’t use the term T3SS to refer to the injectisome as a whole, but rather the protein secretion system at the heart of both the flagellum and the injectisome.
The paper doesn’t really deal with the evolutionary origin of the flagellum and as such there doesn’t seem to be any reason to cite any of the articles where Nick Matzke is a co-author. It does contain a nice figure 2 however, that depicts the homologous components shared between the injectisome and flagellum, of which the T3SS is merely a part.
On another related note, Matzke anticipated the possibility that T3SSs in the injectisome would phylogenetically derive from flagella in his 2003 article, in Section 3.2.2. Are nonflagellar type III secretion systems derived from flagella?