https://biblio.ugent.be/publication/8752596/file/8752597.pdf (2022)
The genotypic and phenotypic characters could both be ancestral to avemetatarsalians; alternatively, both evolved independently in theropods and pterosaurs, or the genes are ancestral and the phenotypic expression occurred independently in the two groups. Our ancestral-state estimations (Extended Data Fig. 9e) reveal that the most parsimonious scenario is that feathers in the avemetatarsalian ancestor had melanosomes with different geometries. This is consistent with a single, deep evolutionary origin for this feature, whereby critical shifts in the genetic machinery facilitating plasticity in melanosome shape occurred in the common ancestor of pterosaurs and birds. Key genomic controls on melanin-based colouration that define the plumage colours of theropods and fossil and extant birds were therefore already in place in early-diverging avemetatarsalians in the Middle to Late Triassic.
Alternatively, I am suggesting that the most parsimonious scenario is that the stage IIIa feathers of short bony tailed pterosaurs (eg Tupandactylus pterodactylid) developed in their own pterosaur lineage and later developed into the feathers of short bony tailed scansoriopterygids (eg epidexipteryx).
There is no need to imagine feathers in an avemetatarsalian common ancestor (and corresponding ghost lineage) since dinosaurs did not have feathers.
Data availability
Additional data on melanosome geometry and the character matrix used in the phylogenetic analyses are available in the Zenodo.org data repository at https://doi.org/10.5281/zenodo.6122213. SEM images and samples are available from the corresponding authors on request.
Data:
This link brings up a very helpful spreadsheet which shows that stage 5 feathers were only on the pterosaur, ornithomimids, oviraptors and paraves.
But ornithomimids and oviraptors are flying or secondarily flightless members of Paraves.
In summary, stage 5 feathers are only on pterosaurs and within Paraves.
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