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Photo#1457112
Stem borer, Phlox

Stem borer, Phlox
Red Oak Prairie, Allamakee County, Iowa, USA
July 29, 2017
A few examples of this fly's sign were found on Phlox pilosa in a prairie remnant. At the time I came across them (late July), the puparia were already spent, suggesting the larvae are active in spring or early summer.
As is evident here, it appears some shoot wilting or dieback may be associated with the larva's stem-boring activities.
Another one apparently in need of rearing, as I can find no prior records of internally feeding agromyzids in Phlox.

Stem cut open lengthwise for these photographs

Arrow indicates puparium (spent) inside stem

Images of this individual: tag all
Stem borer, Phlox Stem borer, Phlox

More phlox borers
Today I finally picked the garden phlox stems shown here (leafminer #153), and as expected there are signs of something feeding inside--a narrow, winding trail in the pith, as you've found in some Melanagromyza spp. The gallery goes into the base of the stem and probably into the roots. I pulled up part of the underground portion, but for all I know the larvae are immature and would come back up in new stems in the spring to complete development. We shall see!

 
Excellent
I'll be very interested to know what it turns out to be. I wonder if it would be worth it to dissect the roots from one of the affected plants to see if you can find the culprit...that would doom the animal of course (unless you could transfer it to the roots of another plant), but at least you'd have some sense of what the animal looked like and could narrow down its identity to order at least.

Are you able to clearly observe the midrib mine transitioning into a tunnel in the pith of the stem? Just so as to establish that there aren't two different creatures at work here. I know that's been very tricky to do as I've investigated this sign on Ageratina altissima:

...the first plant I found with a leaf like this (in 2018) had a slender lizard beetle larva in a tunnel in the stem, but it wasn't at all clear if that larva was also responsible for the damage to the leaf. Earlier this year I found a mordellid larva in one such affected leaf and so I now suspect mordellids are responsible for the midrib/petiole tunneling I'm seeing on white snakeroot. And today I found a mordellid larva in a white snakeroot stem, so I know they are in the stems at least sometimes, too. But I still haven't found that hypothetical nice neat example where I follow a petiole mine into the stem and the tunnel in the pith ends with a mordellid larva munching away. That would really tie things up nicely...

 
Well...
There aren't enough of them for me to be willing to sacrifice one to try to get a look at the larva, but at your prompting I just investigated the leaf-to-stem connection. Although I'm unable to perform a clean dissection of a phlox stem and midrib with the tools I have, I verified that there is no visible tunnel in the pith immediately above the mined leaf, while there is one right at the node where that leaf comes out, and it continues down from there.

On another note, this week I noticed a 2-cm length of an Onoclea sensibilis pinna rachis that had turned brown, right up to the junction with the main rachis. I opened that up and found what seems to be a parasitoid wasp larva inside. A few cm away in a seemingly unaffected portion of the same rachis, I can see what seems to be a 3-mm-long larva inside when I hold the frond up to the light. So keep an eye out for inconspicuous internal fern feeders!

 
I love the sound of your fern find
and would love to come across something like it. Will keep an eye out.
Sure does sound like the leaf miner and stem borer on your phlox specimens are one and the same as you suspected. I hope you can figure out what it is!

The puparium reminds me of Ophiomyia...
but I wouldn't count on that. There was no externally visible mine in this case, correct?

 
Correct
A conspicuous agromyzid-sized hole in the stem (the adult's escape route, apparently) right by the puparium, and some wilting/dieback of the shoot above the puparium, were the only external signs I noticed.

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