Any major gaps left in the vertebrate family tree?

Not in the LRT.
While new vertebrate taxa are being published every week, categorically none of these are completely new and unheard of. New taxa are all falling into or between established clades.

There are no large gaps or weird enigmas
in the vertebrate fossil record, according to the the large reptile (LRT, 1663+ taxa). We know where turtles, catfish, snakes, whales and pterosaurs came from. Sure, I’d like to find someone report a short-fingered bat in the Cretaceous (Fig. 1), but that won’t come as a surprise when it happens. We already have the bookend taxa for that discovery.

Figure 1. Subset of the LRT focusing on the clade of colugos, pangolins and bats.

Figure 1. Subset of the LRT focusing on the clade of colugos, pangolins and bats.

Now only microevolution separates one taxon from another
and one clade from another. Every taxon in the LRT has sisters and ancestors back to Cambrian chordates. All sisters are more or less visually similar to one another.

Now all we have to do
is to continue slipping new taxa between established taxon pairs already in the LRT.

The only issue that remains is one that may always remain…
We don’t have, nor will we ever have, transitional fossils from the genesis of every transition (Fig. 1). Most of these are lost to time, or were never fossilized. What we do have are later-to-extant representatives of these transitions. And that’s okay.

That’s where systematics and taxonomy stands in Spring 2020.
The hard work is done. Fossil and extant taxa nest together. Taxon exclusion has been minimized in the LRT due to its wide gamut.

Unfortunately, paleo moves at a snail’s pace,
so there are still workers who cling to invalid hypotheses like pterosaur are archosaurs, caseids are pelycosaurs, or reptiles began with Hylonomus. Vancleavea is still on several archosauriform taxon lists. Multituberculates are still considered egg-laying mammals.

All of this nonsense
can stop now. Just add taxa. The LRT provides a suggestion list.

Run your own tests
to validate the LRT or invalidate it. Don’t trust it. Test it. Just make sure your observations are insightful and true, your reconstructions (show your work!) minimize freehand influences, and your taxon list is wide enough to include all possible candidates. Then share it with us when you have something to present.

A good scientist
attempts to falsify his own and other conclusions. To that end, scoring changes and reevaluations have been a part of the LRT since its inception nearly a decade ago.

Thank you
for your readership, your suggestions and your criticisms.

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