Rightly or wrongly, I’ve taken Ewert’s paper to comment on the incompleteness of common descent explanations via nested hierarchies, rather than its denial. It’s certainly useful to view it that way. @Ashwin_s is right to say how many have taught (eg on BioLogos) that the prevalence of neat nested hieracrchies is strong evidence for common descent, and I’ve pointed out in reply that they were considered strong evidence of the principle of plenitude (Linnaeus) before evolution was ever proposed.
In other words, even perfect nested clades do not necessarily show common descent, and I suspect the “Creationist” application would be that if they are sufficiently disrupted by other mechanisms not easily explained, the application to CD is far less secure.
But whatever additional explanations are found for apparently non-inherited features, if they are suffciently common, they point to other possible causes being severely underestimated, just as the theory of divergent human races separating from common stock is undermined by genetic evidence of extensive interbreeding. Drawing an anthropological tree like the Eugenicists is simply a false understanding of even a single human race.
Joshua’s example of the human race might, I think, possibly be misleading. What human nested hierarchies we find are the result of tribalism and geography and, as he implies, are disrupted by interbreeding (hence genealogical Adam). Humanity is a freely breeding single population, for all its genetic variation.
Now, the same is certainly true of closely related species: they’ve had a glut of reclassifying bird species since genomics, and our own species is known to have hybridized with Neanderthals etc, so that it’s hard to define the species, but easy to spot incomplete lineage sorting, etc. Likewise, many bird of paradise species are hybrids (thus demolishing the long-favoured sexual selection theory of their evolution, since females regularly breed outside the genus, let alone outside the most perfect displayers).
But these ideas seem far less tenable at higher taxonomic levels, where diagnostic features even of orders or classes crop up in the wrong groups: the recent big example was the diagnostic pelvic anatomy of the two major dinosaur groups suddenly being overturned after a century - the explanation being that it must have evolved twice, tens of millions of years apart. The diagnostic homology is no longer a homology at all.
On The Hump, whenever my attention happens to be drwan to a taxon, I like to look at its phylogeny. It virtually always turns out that the origin is disputed. There are two or more entirely different proposals for turtle origins. Three for the pterosaurs. And the reason for dispute is that they share diagnostic features (or in some cases genetic markers) with groups that supposedly separated millions of years before - no incomplete lineage sorting there, surely, no chance of hybridization, and horizontal gene transfer, currently, is though to be minimal in these higher animals.
Convergent evolution is left, but is, after all, only an epicycle to explain away the particular anomalies left when you finally plump for one phylogeny over its rival theories. Even its major proponent, Simon Conway Morris, proposes some kind of emergent laws governing, it which are no less mysterious and undemonstrated than anything Winston Ewert might have in mind.
One of my favourite examples is the bat, or bats. The first theory was that they derive from primates, based on the anatomy and brain structure of diurnal bats. But the oldest bat fossils are just as specialized as the modern nocturnal echo-locating bats, which seem derived from insectivores. Needless to say, the trail disappears at the beginning of both groups, and the phylogeny is “disputed.” That is, where it matters the nested hierarchy doesn’t exist until you create it.
Apparently genetic studies affirm the monophyletic nature of both groups of bats, and the conclusion is that they must have diverged very early for one group to have echolocation, insectivorous habits and nocturnal lifestyle, and the other group to be much bigger “winged primates”, with good vision, eating fruit and flying by day. Yet the first fossil of these larger, and so more likely to be fossilized, bats is 15 million years later than the oldest bat (which looks to be able to echolocate).
Personally, I doubt if anyone would consider these two groups to be related apart from the uncomfortable fact that they both have the same wing-plan.Nobody, it seems, is willing to bet on neutral change or natural selection producing such a specalisation twice, when birds and two branches of pterosaurs had quite different solutions for flying.
But on current theory, there must be a nested hierachy, and it seems one has to choose more or less arbitrarily what major anomalies to ignore. The decision to make bats monophyletic seems to be based on the human decision that a clade can include apparent insectivore descendants and apparent primate descendants, so long as the wing plan and some gene families are similar. Bat wings can’t evolve twice - though echolocation can, but nobody derives bats from dolphins, of course. That would be absurd.