this post was submitted on 12 May 2024
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I feel inappropriate near all the very universal questions here, but as a paleontologist specialised in some reptilian groups, the question would probably be "where the fuck do turtles come from?!" The thing is that fossil evidence points to different answers when compared to genetic evidence, and thez separated long enough from other extant groups that we keep on having new "definitive" answers every year
Genomics makes this answerable though? It's just a matter of whether DNA is preserved or not in fossils. Genomics is more reliable than comparive anatomy. Comparative genomics can accurately place turtles in animal phylogeny. Sorry if I misunderstood your post. Or am I wrong here?
In phylogeny, genomic is just another tool. The point is that turtles are os course animals, but they do branch off of different reptile groups if you look at morphological evidence (which includes fossil data) or at molecular (genetic) evidence (which only includes extant species). This is not something frequent, as usually molecular evidence tends to strengthen previous morphologically established evolutionary relationships. And even though molecularists are more numerous today, their methods are neither better or worse than anatomy.
Phylogeny is not as straightforward as some people make it seem, and especially molecular phylogeny tends to rely on abstract concepts that can't always be backed up by biological evidence (I'm not saying it's wrong, it's very often very good, juste that a lot of people doing it do not understand the way it works, and thus can't examine the process critically).
And so turtles' origin are still very much an active debate!
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.