the fact that the authors conclude that it may be the result of convergent loss prove that even according to evolution theory there is no problem with non-nested hierarchy.
It wouldn't be a non-nested hierarchy if there was a loss in those lineages.
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It is also worth mentioning that the authors concluded that the neural systems evolved independently:
"Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of ‘classical’ neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals."
https://www.nature.com/nature/journal/v510/n7503/full/nature13400.html
so your claim about nested hierarchy as evidence for evolution isnt true even by the experts in the field. but you are welcome to believe that it's false.
The experts in the field are the ones who claim that the nested hierarchy is evidence for evolution:
"It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life."
Emile Zuckerkandl and Linus Pauling, discussing the possibility of the twin nested hierarchy before the first molecular phylogenies had been made.
(1965) "Evolutionary Divergence and Convergence in Proteins." in Evolving Genes and Proteins, p. 101.
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