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The emergence of an ecological community in evolutionary time is the result of species evolution and coevolution. In species rich and functionally diverse communities, there are a multitude of alternative pathways along which emergence could proceed. Nevertheless, analysis of alternative pathways for paleocommunities spanning more than 13 million years of the Permian-Triassic of the Karoo Basin of South Africa, suggests that pathways actually taken represent a small subset of the total available. This leads to a narrow representation of the total number of communities possible given a specific number of species and level of functional diversity. Furthermore, the paleocommunities were always superior to structural alternatives of equal complexity, in terms of community global stability (the number of species that can coexist stably and indefinitely). Such optimization could indicate a selective process during the formation of types of communities, or simply be emergent from the coevolutionary framework. Here we present ongoing work to support an emergent process by which many alternative types of communities may form constantly on ecological timescales, but where few are stable and persistent on longer timescales. This leads to the compositional stability of paleoecological units often noted in the fossil record, and the apparent incumbency of long-lasting lineages. The aftermath of mass extinctions present opportunities to test this hypothesis, because previously persistent communities are replaced by newly emergent ones, and the emergence process itself can be extended to geological timescales because of ongoing environmental instability, and the time required for the reformation of coevolutionary relationships and functional structures. Such is the case in the aftermath of the Permian-Triassic mass extinction, when Early Triassic paleocommunities in the Karoo Basin were sub-optimal compared to alternative, hypothetical histories. Understanding long-term ecological persistence is crucial to our understanding of the modern anthropogenically-driven environmental crisis. Modern ecosystems are the documented products of geological and evolutionary history. Species acclimatization and adaptation to ongoing changes are not necessarily guarantees of the future persistence of the resulting reorganized systems. It will become critical to determine if the biosphere has already turned down new ecological and evolutionary pathways, or is still operating in the capacity of the pre-Anthropocene system.