Can two distinct large isolated life pockets on the planet evolve independently and then merge without driving one another to extinction?

Question

In the geological history of my planet, the plate tectonics resulted in the assembly of a kind of "ring supercontinent", that completely encircled a portion of the ocean and isolated it from the rest of the planet for a hundred million years or so.

It happened very shortly (geologically speaking) after the life on the planet discovered the joys of having vertebrae (Roughly analogous to the Silurian-Devonian or so in the Earth's history), and this configuration of continents lasted long enough that the species in the interior ocean and on the outside have been evolved separately, which had resulted in the rise of two distinctly different convergently evolved bony vertebrate lineages (Among the whole bunch of other parts of the biosphere), that have quite distinct anatomical structures that will in the future evolve into true bony skeletons, which in turn will result in the planet having two distinctly different types of land animals.

Sometime after that, the continents supposedly broke up and allowed the two biospheres to mix up. At the time of the continental break up the interior ocean had a surface area of about 3\5 of the Atlantic.

Is there a way for them to do that in such a way that they both biospheres survive this mixing up, without one lineage out-competing the other into oblivion?

Them coming out of mixing uneven is fine, my current worldbuilding states that descendant species from the inside of the continental circle consist only about 30% of all the vertebrates.

If you don't think so, please provide the next best thing that could result in drastically different skeletal structures of vertebrate animals (The kind I seek doesn't have a different amount of limbs or anything like that, but the shape of the bones and in particular the anatomy of the skull and jaws is entirely different to the point that I don't think that one could plausibly evolve out of the another, mostly the skull, since even 500 million years later, basically all vertebrate life on Earth still shares same general skull anatomy with those first 420 million-year-old jawed fishes, so I came to the conclusion that the point of divergence should be then or earlier).

Answer 1

One side will probably outcompete the other, with a few exceptions.

The analogous real situation I can think of is the Great American Interchange, when North and South America became connected and allowed interchange of fauna.

https://en.wikipedia.org/wiki/Great_American_Interchange

In general, the initial net migration was symmetrical. Later on, however, the Neotropic species proved far less successful than the Nearctic. This difference in fortunes was manifested in several ways. Northwardly migrating animals often were not able to compete for resources as well as the North American species already occupying the same ecological niches; those that did become established were not able to diversify much, and in some cases did not survive for long.[78] Southwardly migrating Nearctic species established themselves in larger numbers and diversified considerably more,[78] and are thought to have caused the extinction of a large proportion of the South American fauna.[61][79][80] (No extinctions in North America are plainly linked to South American immigrants.[n 10]) Native South American ungulates did poorly, with only a handful of genera withstanding the northern onslaught.

There are just a few successful South American natives in North America. The opossum is my favorite because marsupials take so much flak for being primitive and unworthy, but the opossums have been doing great. Shout out to the opossum! - and this hard to find little monograph which is a hidden gem. http://www.wildlifeservices.org/PDFS/TheOpossum.pdf

If this is for a fiction it will be more fun to have the losers represented as a few remaining species, their differences from the majority species being more interesting an d easier to convey because these species are exceptional and few in number - although (like the opossum!) represented by many individuals.

Answer 2

To make this possible, I think the easiest way is to make your two clades of animals occupy different niches. At least to start with.

If a member X of Clade A specialises in something that no member of Clade B can do, perhaps because the niche simply doesn't exist in the domain of Clade B, the descendants of X could live on even if Clade A is otherwise out competed.

In the case of the Great American Interchange, you had two continents with forests and plains, large grazing animals, carnivores hunting these, and so on. When mixed, they competed on the same playing field, and one side lost.

Make up some circumstance that some inhabitants in one of your oceans cave conquered, let these survive and have the others extinct. This is easy to justify, and has the bonus effect of allowing all decedents to inherit some quirky adaptation to this circumstance.

With this special group in place, you could then let it slowly diversify and start entering other niches.

There are many ways to do this, and these are just a few suggestions:

• Let members of Clade A move up on land! Even if life in water end up dominated by Clade B, they can't out compete terrestrial animals. Nothing stops you from later having the terrestrial animals then reenter the oceans, like in the case of whales. Depending on how your rings are located, this could be facilitated by larger tides and large tidal planes on one side. You don't even have to make the transition to land complete, just make them somewhat amphibious.
• Ocean A has really really deep trenches, Ocean B doesn't. An ecosystem evolves down there which stays unaffected by the extinction of shallower A-life. There is then plenty of time for the deep life to have some animals slowly adopt to the shallows and the competition from B-life, and then spread to both oceans.
• Make a small but robust ecosystem that can spread without competing with the rest. In the tropics of Ocean A, you have small floating "islands" (composed of some fungus or the like), on which sit specially adopted barnacles, or maybe snails, which have incredibly hard shells. These islands are very sensitive to cold, and only survive very close to the equator. There are vertebrates in Ocean A which have co-evolved with these hardened suckers, and can gnaw through or maybe crush their shells. This would also explain the different heads! You could also have further fauna adapting to these islands, maybe become "terrestrial" and live on top of them? As the oceans mix, the islands spread to both oceans. Most animals in Ocean A is out competed, but the islands spread around the equator in the other ocean and the islanders along with them. Some B-life will no doubt eat the Gnawers, but if they can hide inside (or on top) the islands they have some chance of surviving long enough to have time to adopt and then maybe find other niches as well. They could transition to either other shelled things, and maybe end up more general predators?

These are just three suggestions; you could vary them or make up your own niches. You could also have "normal" animals survive on both sides, @Willk mentions the opossum, this is maybe even likely. It's harder to predict though, and not so spectacular. I also think having an isolated echo system survive betters your chances of not ending up with a single specialised species, but something that might actually evolve to make up a fair percentage of the fauna on a global scale.

Answer 3

One simple solution:

The otherwise-inferior group developed flight, the otherwise-superior group did not.