Written by T.K. Sivgin
To gain an understanding of what really happened on this bizarre construct, we must first trace back where everything began. The lack of proper tetrapods as well as the presence of zosterophyle flora and various other clades strongly indicates that all the lifeforms on here descend from species on Earth that were indexed from the Mid-to-Late Devonian, likely Givetian (387.7 to 382.7 Mya) or earliest Frasnian stage to be precise. At least some taxa seem to descend from lifeforms that came a bit earlier or later, though due to the incompleteness of Earth's fossil record it is plausible that some of the clades in question persisted longer or originated earlier than we thought and were also among the Givetian life that was indexed. Signor-Lipps effect and all that. It is quite notable how thorough the aliens were when indexing our planet's past biota, which lends further credence to the Rhynia starting out as some sort of conservation project. Either that or a ridiculously elaborate zoo.
In terms of plant-life this period was especially interesting as right at the start of the Givetian the first permanent greenery and tree-like plants had evolved in a massive radiation of both familiar and bizarre, extinct forms, the botanical equivalent of the Cambrian explosion. Many of the strange forms would gradually go extinct towards the end of the period but were still thriving during the Givetian and would thus have been indexed by the aliens, a paleobotanist's wet-dream.
The most common flora during this time would have been "primitive" plants that were still spore-bearing. The most obvious and primitive flora to be found would be non-vascular bryophytes, better known as mosses. Out of these had by this time already evolved the vascular plants, which can be roughly split up into an exarch-lineage (which developed their tracheids from the outside to the inside of the body) and an endarch-lineage (which did the opposite).
The exarch-branch consisted of plants roughly resembling (and being related to) modern club-mosses. The oldest known types of these would have been organisms like Baragwanathia above, which despite being Silurian in age already looked disturbingly similar to the modern ground pine (Lycopodium). While Baragwanathia proper is only known up until the Eifelian, the stage immediately preceeding the Givetian, it is save to assume that plants of this type would have still lived during this time as they still do today. Indeed, ground pine-like plants are reported all throughout Dome 4.
Very bizarre early members among the exarchs were the Zosterophylla, which are thought to have been stem-group lycophytes. These were generally creeping plants similar to Lycopodium, but are unique for various reasons. For one they are one of, maybe the only major plant group that went extinct during a global mass extinction, the Kellwasser-Event at the end of the Frasnian. They were also the only plant-group to exhibit any sort of bilateral symmetry, both in their branches and stems. Thrinkophyton formosum above is exemplary of this. Zosterophylls were also the only plants ever which had an oval-shaped stele (the central part of the body), which is also a sign of internal bilateral symmetry. Zosterophylls were to other plants what starfish are to chordates. Zosterophylls were largely leafless plants, similar to earlier plants like Cooksonia, though unlike that genus, the ends of their axes did not end in sporangia, instead the buds grew alongside the stem and branches. At least the species Sawdonia acanthotheca showed early stages of microphyll-leaf-evolution, while Trichopherophyton from the Rhynie Chert shows that at least some of them had fine hairs on their bodies. Before their extinction the zosterophylls were some of the most abundant plants in the Devonian flora and thus also seem to have been indexed.
The actual lycophytes were much more diverse during this period than they are today, with genera such as Colpodexylon, Leclercqia and Cyclostigma, though they had not yet grown to the large sizes of the famous scale-trees of the Carboniferous. At least one genus, the Protolepidodendropsis here, did at least grown to approximate sizes of around 4 meters.
Among the endarch-lineage the most primordial group were the rhyniophytes, such as the famous Cooksonia from the Silurian or Rhynia from the Early Devonian. The youngest member of this group, Stockmannsella, survived until the Eifelian like Baragwanathia. It is possible some of these survived into the Givetian and could have been indexed by the aliens, but so far we have no evidence of this. The only flora so far reported from the ruined Dome 1 does intriguingly bear some resemblance to Aglaophyton above, though this needs further investigation before anything substantive can be said.
Through transitional forms such as Psilophyton emerged groups still familiar to us such as ferns, though in this time they were mostly odd stem-group members, as crown-group ferns would first truly appear in the Triassic. One such group of stem-ferns were the cladoxylopsids, of which one member that appeared right during the Givetian would have been Wattieza, generally agreed to have been the oldest known tree-like organism, potentially standing up to 8 meters tall. It can be best imagined as a prehistoric tree-fern. Many others of these stem-ferns would have not been ground-living plants, but epiphytes growing on top of larger plants. Close relatives of ferns, the horsetails, were also present, but they did not yet grow to giant sizes as they did in the Carboniferous.
Among the first tree-like organisms would have also been progymnosperms such as Archaeopteris (not to be confused with the dinosaur Archaeopteryx), whose branches you can see above. Progymnosperms were, as the name implies, the ancestors of seed-plants and were predictably still primitive in their reproduction, with simple open seeds. Every other seed-bearing plant known to us, such as seed-ferns, conifers, ginkgos, cycads and especially flowering plants had not evolved yet by this stage and are thus entitely absent from the Rhynia.
Regarding non-plant organisms, it should be mentioned that giant lichen-like organisms such as Prototaxites would have still been around.
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