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Albertonykus's avatar

Vertebrata Phylogeny

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I said I wouldn't be updating the Big Vertebrate Tree, but so long as Drs. Holtz and Merck continue making their course materials available publicly, there's nothing stopping me from updating just its general topology. Taxa in bold have extant representatives. I have graduated from UMD, and do not have inside info on why specific topologies may have been favored over alternative hypotheses.

Edit: No (intentional) changes to the topology here, but I discovered the program TreeGraph for manipulating phylogenetic trees and decided to redo this tree using it. The aesthetics and readability have improved a good deal, I think.
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ArthropodMan's avatar

How did you make all the branches have different lengths rather than all the branches leading into a single column of words?

Albertonykus's avatar

Ah, it's possible to specify the branch length by right clicking and selecting "Edit branch length". The branch lengths will only be visible under "Phylogram/Chronogram view" from the row of options on top.

SpongeBobFossilPants's avatar
Is traditional Gasterosteiformes (including syngnathiforms) monophyletic? I see you use Syngnathiformes here, but I don't know if that's because Gasterosteiformes is polyphyletic or Syngnathiformes is preferred over Gasterosteiformes for some reason.
Albertonykus's avatar
I can't pretend to know anything about actinopterygian taxonomy. I used Syngnathiformes because Merck used Syngnathiformes, and he used it because Betancur-R et al. (2013) used it. However, Betancur-R et al. do state that they found traditional Gasterosteiformes to be polyphyletic and that they instead consider gasterosteids to be members of Perciformes, so that's probably the answer to your question.
SpongeBobFossilPants's avatar
Where are lophiiforms? Aren't they close to tetraodontiforms?
Albertonykus's avatar
This doesn't include all the teleost groups.
ArthropodMan's avatar
It must have taken a ton of research to complete this. Congrats. Though, you forgot Hiakouichthys and nectridean lepospondyls. But I have an even bigger question.

Why do fish only make up 20% of the tree when the majority of vertebrates are fish?
Albertonykus's avatar
This is based largely on a course I took as an undergrad. Because it wasn't a paleoichthyology course, more emphasis was naturally placed on groups that had spawned a greater body of literature (mammals) and the instructors' own research interests (reptiles). "Nectrideans" were excluded because they might not be a monophyletic group (see e.g.: Ruta and Coates, 2007), and Haikouichthys is probably closely related to (if not the same as) Myllokunmingia.
ArthropodMan's avatar
I know nectrideans may not be monophyletic, but why did you exclude a big portion of the lepospondyls is what I'm asking.


I feel like people have a skewed view of vertebrates, that fish are just one group. In reality, the majority of vertebrates past and present are fish. The fish is the default vertebrate. Tetrapods are just weirdly derived terrestrial fish. But anyway.

I can understand the simplification of fish, but I still kinda wish you went further into percifomres. That's just me.

I have a proposal. Instead of Myllokunmingia, how about Myllokunmingiidae which includes both Haikouichthys and Myllokunmingia (as well as Zhongjianichthys)

And why are pederpes and ichthyostega excluded from tetrapoda when they are quite clearly tetrapods?

And one last thing. It's actually quite possible that conodonts are not even vertebrates.
www.researchgate.net/publicati…
Albertonykus's avatar
Again, this is simply a summary of the course materials provided in a class that I took. As such, it was shaped by constraints imposed by the nature of the course and decisions made by my instructors. We covered the existence of "nectrideans" and Haikouichthys, but we didn't go into enough detail about their systematic position to include them in the "summary diagrams" that my instructors compiled. Ichthyostega and Pederpes are not "clearly tetrapods" if you use the crown-group definition of Tetrapoda, which is what we did. (If anything, they are clearly not crown-tetrapods.) We did mention that the position of conodonts is uncertain, but considered that the weight of the evidence was sufficient to tentatively favor them being vertebrates. If I had made this diagram entirely from scratch instead of using the course as a framework, it would probably look slightly different (though I doubt it would be different enough to motivate me into doing it).
ArthropodMan's avatar
I wonder. Why use the crown based definition for tetrapoda over a node based one? I know that your course probably used the crown definition, but I wonder if there was a reason for it.
Albertonykus's avatar
Crown-group definitions are inherently node-based (in this case, the last common ancestor of lissamphibians, mammals, and reptiles and all of its descendants). More inclusive definitions of Tetrapoda are usually stem-based (anything closer to crown-tetrapods than to lungfish) or apomorphy-based (the first ancestor of crown-group tetrapods to have four limbs with digits and all of its descendants).

My instructors aren't fans of apomorphy-based definitions (and neither am I, frankly), mainly because features that we think are distinctive in hindsight have often undergone intermediate stages during their evolution that make it difficult to determine at what point they can be considered to be first present in a clade. As for using the crown-group definition over the stem-based one, the general trend (at least in vertebrate paleontology) is to apply "classic" names to the crown group (as has been done for Archosauria, Lepidosauria, Mammalia, etc.). Additionally, the earliest total-group tetrapods (like rhizodonts) weren't particularly similar to crown-tetrapods, which some might find confounding. In that case, might as well apply the name to the group that we can be certain had all the characteristics we associate with the name, at least ancestrally (i.e.: the crown group). But it's a matter of personal preference in the end. I don't think it's a big deal as long as it's clear which definition is being used.
ArthropodMan's avatar
I get that apomorphy based definitions can be vague at times, but crown definitions aren't perfect themselves, as determining weather an animal belongs to clade or not based on weather it's alive is kinda weird. If pederpes was still alive, we would consider it a tetrapod.

Plus, apomorphy based clades are kind of necessary. Important traits may not have originated with the total group or crown group, but somewhere in the stem group, as is the case with tetrapods. Limbs with digits first appeared in elginerpeton, and appeared in later 'tetrapods' that aren't in the crown group. Some stem members such as pederpes have quite robust walking limbs. So, an apomorphy based clade that includes some but not all the stem group is necessary. This clade already exists, it's called stegocephalia. But, I feel like that stegocephalia should just be tetrapoda and the crown group can be eutetrapoda.
Albertonykus's avatar
Sure. Whatever naming scheme we use, there will always be some arbitrary metric involved in deciding how we apply it. That's why I don't consider it a big deal that different people use the term Tetrapoda differently.

However, I don't think apomorphy-based clades are necessary. We can discuss the acquisition of key features without defining clades based on apomorphies. For instance, we could name a node-based clade based on the last common ancestor of Pederpes and crown-tetrapods and say that increased terrestrial habits likely arose in that clade, instead of defining the clade based on features supposedly associated with terrestriality (and unnecessarily delimiting what was almost certainly a gradual process).
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TheDubstepAddict's avatar
No ornithoscelida?
TheDubstepAddict's avatar
What? Shouldn't the germanodactylids be closely realated to the dsungaripteroids? If not can I get the paper about it?
Albertonykus's avatar
The pterosaur section looks like it's based on the Andres topology.
Sombraptor's avatar
Absolutely amazing. Just a heads-up, but Barbourofelidae is in bold when it shouldn't be...unless Drs. Holtz and Merck taught you something the rest of us don't know lol.

Also no Hyaenidae coming out of Feliformia.
Albertonykus's avatar
Good catch, thanks. It's been fixed. Hyenas are part of Viverroidea.
Sombraptor's avatar
Are they now? Huh. Guess I have to refresh my mammal phylogeny lol. And no worries, glad to be of help.
SpongeBobFossilPants's avatar
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