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I was trying to figure out the early geological/biological history of the world I'm creating, and I was wondering about the development of early life. Basically, I've envisioned a world where Eukaryotic cells are the most complex form of life, but at the same time, a global catastrophe comparable to the Siberian Traps has occurred. Having researched that, I've come across the fact of water stagnation across entire oceans due to lack of water currents in the wake of climate change. Although I've decided for this point in time to be a handy moment for the evolution of photosynthesis, it won't do much good if all life's already died out by this point. So, basically...

In the event of ocean stagnation, where could Eukaryotic life be capable of surviving?

Vents? Rivers?

A quick note, in spite of the alien world, for the sake of expedience, the Eukaryotes possess Earth-like biochemistry and use oxygen for respiration.

Any answers would be greatly appreciated.

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Some eukaryotes can survive anaerobically. Many yeasts.

Anaerobic Eukaryotes

You could have eukaryotes thriving in fresh water, and if you already have algae or lichens etc surviving on land, you could have eukaryotes among them. They might survive in the wave-tossed top layer of the ocean, assuming there's enough oxygen in the air.

They don't have to thrive as well as they do now, to evolve the things that let them expand so well later.

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even in a situation where oceans have become relatively anoxic, highly oxygenated water in springs, streams, rivers emptying into deltas will persist.

there will usually be redoubts of habitable conditions here and there, even in the midst of a mass extinction event, otherwise such extinction events would be total.

for example, even during the snowball earth epoch which shortly preceded the proliferation of animal/plant life in the ediacaran, during which ice covered the planet all the way to the equator, there must have been some atmospheric venting to account for the persistance of aerobic heterotrophs existing under the sea during all that interval, which is estimated to be in the millions of years.

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