this post was submitted on 12 May 2024
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Maybe we're not talking about the same thing? I was thinking about the diapsid debate, where genetic evidence is overwhelmingly strong in favour for diapsid evolution Mitochondrial DNA evidence: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC24355/ Micro RNA evidence: https://pubmed.ncbi.nlm.nih.gov/21775315/
Tbh a core multi gene ML tree to all other reptiles would prove it beyond a shadow of a doubt, maybe someone's done that already but I haven't been able to find it.
The diapsid part is very likely indeed, as fossil skulls of early stem turtles do show some temporal openings ( https://www.annualreviews.org/content/journals/10.1146/annurev-ecolsys-110218-024746 ) The point is more where do they nest within Diapsida, more closely to the Lepidosauromorpha, or to the Archosauromorpha, and where precisely if within one of those clades. The point is that can't quite be proven using only extant species, whether by DNA or morphological evidence. And concerning ML, the methodology is often criticised, not because it's bad, but because it's opaque and thus it is difficult to justify and understand as a process
Three robust genetics papers using different sequences and genes, each time place it as a sister group to Archosauria:
248 nuclear genes (187,026 nucleotide sites): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473239/
1145 ultraconserved elements (UCEs) and their variable flanking DNA: https://royalsocietypublishing.org/doi/10.1098/rsbl.2012.0331
1,113 single-copy coding genes, robustly indicated that turtles are likely to be a sister group of crocodilians and birds: https://www.nature.com/articles/ng.2615
This level of genetic evidence is an overwhelmingly strong signal, regarding relationships and recent common ancestry to extant species. I would say it is undeniably strong. You cannot possibly get evolutionary convergence over this many genetic loci.