Since it appears, you seem to think that the expert opinion, or interpretation must definitely be right, I'll allow the experts to point out to you,
where they do get it wrong.
On universal common ancestry - sequence similarity and phylogenetic structure
Universal common ancestry: The qualitative evidence and need for a formal test
When biologists attempt to reconstruct the phylogenetic relationships that link a set of species, they usually assume that the taxa under study are genealogically related. Whether one uses cladistic parsimony, distance measures, or maximum likelihood methods, the typical question is which tree is the best one, not whether there is a tree in the first place.
This is the question I set out to answer: Is there a universal tree — or, more broadly, a universal pattern of genetic relatedness — in the first place?
Several researchers have recently questioned the nature and status of the theory of UCA or have emphasized the difficulties in testing a theory of such broad scope. For example, Ford Doolittle has disputed whether objective evidence for UCA, as described by a universal tree, is possible even in principle:
Indeed, one is hard pressed to find some theory-free body of evidence that such a single universal pattern relating all life forms exists independently of our habit of thinking that it should.
This sentiment was echoed also by K&W, who concluded that
a "formal demonstration of UCA … remains elusive and might not be feasible in principle.". Such criticisms of UCA point to a need for a formal test, similar to the formal tests of fundamental physical theories like general relativity and quantum mechanics.
Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians
Introduction
Phylogeny is the cornerstone of comparative biology, and interpretations of phenotypic evolution hinge on accurate hypotheses of organismal relationships (Felsenstein 1985). Transcriptomic and genomic sequences offer a nearly overwhelming source of information for inferring relationships, with some studies employing hundreds of genes.
Despite great potential, phylogenomics has thus far failed to confidently resolve relationships of many animal groups (Dunn et al. 2014). Inferring relationships among major metazoan lineages (i.e., Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera) has been particularly difficult, with numerous recent studies recovering conflicting phylogenetic topologies
In recent years, systematists have faced many theoretical and methodological challenges associated with analyzing high-throughput sequencing data for phylogenetic inference, and a major bottleneck for modern phylogenetic studies is the analysis of data, rather than the generation of sequences. Modern phylogenomics requires a new set of expertise and methodologies compared with phylogenetic studies with only one or a few genes.
Rethinking phylogenetic comparative methods
...unresolved challenge permeates not just tests for discrete character correlations, but nearly every method of finding associations in comparative methods
On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
Sequence similarity and homology are not equivalent
One common thread among the various arguments for common ancestry is the inference from certain biological similarities to homology. However, with apologies to Fisher, similarity is not homology. It is widely assumed that strong sequence similarity indicates genetic kinship. Nonetheless, as I and many others have argued , sequence similarity is strictly an empirical observation; homology, on the other hand, is a hypothesis intended to explain the similarity. Common ancestry is only one possible mechanism that results in similarity between sequences.
Colin Patterson made a similar argument, explicitly pointing out that statistically significant sequence similarity does not necessarily force the conclusion of homology:
… given that homologies are hypothetical, how do we test them? How do we decide that an observed similarity is a valid inference of common ancestry? If similarity must be discriminated from homology, its assessment (statistically significant or not, for example) is not necessarily synonymous with testing a hypothesis of homology.
How, then, would we know if highly similar biological sequences had independent origins or not? In all but the most trivial cases we do not have direct, independent evidence for homology — rather, we conventionally infer the answer based on some qualitative argument, often involving sequence similarity as a premise.
