Tuatara genes provide false-positive links to mammals

Preamble:
Genomic (gene) studies think they are unlocking secret doors
to understanding vertebrate interrelationships. Sometimes they do the opposite. Wide gamut phenomic (trait) studies show that gene studies over deep time introduce invalid hypotheses of interrelationships. So, worse than useless, gene studies (like today’s example) confuse readers and workers with false positives, false hopes that claim to be true, but are not valid when put to the test.

So why are they published?
Because gene studies work great over shallow time. Ask any prosecutor or Ancestry.com.

Gemmell and Rutherford et al. 2020 report:
“The tuatara (Sphenodon punctatus)… [is] A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes.”

In a competing phenomic study (the large reptile tree, LRT, 1717+ taxa; Fig. 2) the lepidosaur, Sphenodon (Fig. 1), is simply the last living proximal outgroup taxon to living squamates. On the other hand, tuataras and mammals share a last common ancestor all the way back in the Viséan, at the last common ancestor of all reptiles, Silvanerpeton.

Gemmell and Rutherford et al. continue:
“Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago [Earliest Triassic].”

This timing is confirmed by the LRT, but fossils generally represent periods of wide radiations, not moments of origin.

“This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features.”

Phenomic studies do not support a mammal connection other than at the very base of the Reptilia (see the LRT).

“The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation.”

False positives are not valuable resources. They steer readers and workers wrong. Gene studies too often deliver false p;positives compared to trait-based studies over deep time.

From an online story from phys.org with quotes from the authors.
“The tuatara genome contained about 4% jumping genes that are common in reptiles, about 10% common in monotremes (platypus and echidna) and less than 1% common in placental mammals such as humans,” said Professor Adelson.

“This was a highly unusual observation and indicated that the tuatara genome is an odd combination of both mammalian and reptilian components.”

“The unusual sharing of both monotreme and reptile-like repetitive elements is a clear indication of shared ancestry albeit a long time ago,” said Dr. Bertozzi.”

Or… this is a false positive. Not sure why false positives keep creeping in to gene studies, but they do.

Colleagues: Don’t publish genomic studies unless they are confirmed by phenomic studies.

References
Gemmell NJ, Rutherford K., Prost, S. et al. 2020. The tuatara genome reveals ancient features of amniote evolution. Nature (2020). https://doi.org/10.1038/s41586-020-2561-9 DOI: 10.1038/s41586-020-2561-9 , www.nature.com/articles/s41586-020-2561-9

https://phys.org/news/2020-08-dinosaur-relative-genome-linked-mammals.html?fbclid=IwAR1VjTxtCI8Yd9VrUIAbuwxDmEhOM1q27WFueBbt1KIo062qKi2UqNnvzX0

https://www.researchgate.net/publication/342666056_Bird_phylogeny_false_positives_detected_in_a_gene_sequencing_study