Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny - Evolution News & Views

Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research.

Evolution News and Views
Evolution NEWS
 

Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny

We've recently discussed different genetic studies on primate relationships were finding contradictory evolutionary trees. As discussed, one recent study found data that conflicted with the standard primate phylogenetic tree, reporting that "for ~0.8% of our genome, humans are more closely related to orangutans than to chimpanzees." We then commented:

0.8% of our genome might not sound like a lot, but that equates to over 20 million base pairs. That's means that over 500 times more raw genetic information than was used in the PLoS Genetics paper (to purportedly create a "robust new phylogenetic tree") is supposedly pointing in the wrong phylogenetic direction.
Since that time, another paper has been pointed out to me that shows that even far more genetic data is contradicting the standard evolutionary phylogeny of humans and apes. A 2007 article in the journal Molecular Biology and Evolution states:
For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place.

(Ingo Ebersberger, Petra Galgoczy, Stefan Taudien, Simone Taenzer, Matthias Platzer, and Arndt von Haeseler, "Mapping Human Genetic Ancestry," Molecular Biology and Evolution, Vol. 24(10):2266-2276 (2007).)

The article goes on to state that "[t]he human genome is a mosaic with respect to its evolutionary history." In other words, some parts of the genome tell one evolutionary story while others tell a different, contradictory story. Our genome is not painting a consistent picture of common descent. The paper continues:
However, with both amount of data and number of studies increasing, the crux of the matter emerges. Regardless of the type of phylogenetically informative data chosen for analysis, the evolutionary history of humans is reconstructed differently with different sets of data. (internal citations omitted)
This might sound quite bad for common ancestry. But of course the purpose of the article isn't to challenge common ancestry but to save it through ad hoc explanations of this bad data. The article explains away the contradictory data in this way:
To understand why regions in the human genome can differ in their evolutionary history, it needs to be acknowledged that genetic lineages represented by DNA sequences in the extant species trace back to allelic variants in the shared ancestral species. In here, these variants persist until they join in their most recent common ancestor (MRCA). Some genetic lineages, however, do not coalesce in the progenitor exclusively shared by humans and chimpanzees. They enter, together with the lineage descending from the gorilla, the ancestral population of all 3 species, where any 2 of the 3 lineages can merge first. Thus, in two-thirds of the cases, a genealogy results in which humans and chimpanzees are not each other's closest genetic relatives. The corresponding genealogies are incongruent with the species tree. In concordance with the experimental evidences, this implies that there is no such thing as a unique evolutionary history of the human genome. Rather, it resembles a patchwork of individual regions following their own genealogy. (internal citations omitted)
So now, when a gene points in the wrong evolutionary direction, evolutionists just assume (quite conveniently) that the allele in question didn't become fixed into the population of our ancestors at the same time as most of the rest of the genome. Yet another ad hoc epicycle is used to explain away why a whopping "23% of our genome" does not place humans as most closely related to chimpanzees, contradicting the standard evolutionary tree.

Is the statement that "[t]he human genome is a mosaic with respect to its evolutionary history" just a sanitized way of saying 'vast portions of our genome tell contradictory stories about our alleged ancestry with apes'?